LYRM7

UniProt ID: Q5U5X0
Organism: Homo sapiens
Review Status: INITIALIZED
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Gene Description

LYRM7 (LYR motif-containing protein 7; also MZM1L/C5orf31) is a small mitochondrial-matrix LYR-family assembly chaperone for respiratory Complex III (cytochrome bc1 / ubiquinol-cytochrome c reductase). It acts as a dedicated chaperone for the Rieske iron-sulfur protein UQCRFS1, binding and stabilising UQCRFS1 in the mitochondrial matrix prior to insertion of its [2Fe-2S] cluster and the subunit's translocation and incorporation into the late Complex III dimeric intermediate in the inner membrane. Its LYR motif recruits the Fe-S transfer cochaperone HSC20 (HSCB), coupling the UQCRFS1-LYRM7 intermediate to the ISCU-HSPA9-HSC20 cluster-delivery machinery. LYRM7 is non-catalytic and is the human ortholog of yeast Mzm1. Loss-of-function variants cause mitochondrial complex III deficiency, nuclear type 8 (a leukoencephalopathy).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005759 mitochondrial matrix
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) propagation placing LYRM7 in the mitochondrial matrix, where it acts as a chaperone. This is directly confirmed experimentally: LYRM7 binds and stabilises UQCRFS1 within the mitochondrial matrix.
Reason: The matrix location is the site of LYRM7's chaperone activity and is supported by direct experimental evidence (IDA, PMID:23168492) and the UniProt subcellular location, in addition to this phylogenetic inference. is_active_in is appropriate for the compartment where it chaperones UQCRFS1.
Supporting Evidence:
PMID:23168492
binding to this subunit within the
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0034551 mitochondrial respiratory chain complex III assembly
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) inference that LYRM7 is involved in Complex III assembly. This is the core biological process of the gene and is strongly supported experimentally.
Reason: LYRM7 is a bona fide Complex III assembly factor mediating the UQCRFS1/Rieske Fe-S protein incorporation step. This is the precise, well-evidenced core BP and is consistent across IBA, IDA (PMID:23168492), IEA and Reactome TAS annotations.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
GO:0044183 protein folding chaperone
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) assignment of a protein folding chaperone molecular function. LYRM7 is a non-catalytic chaperone that binds and stabilises (holds) its client UQCRFS1, so a chaperone MF is the correct, most informative non-catalytic molecular function.
Reason: The chaperone MF is directly supported: LYRM7 works as a UQCRFS1 chaperone, binding and stabilising the Rieske Fe-S protein prior to its incorporation into Complex III (PMID:23168492). This is the appropriate MF for this non-enzymatic assembly factor and is retained as the core molecular function; no catalytic activity should be assigned.
Supporting Evidence:
PMID:23168492
works as a human Rieske
file:human/LYRM7/LYRM7-uniprot.txt
Assembly factor required for Rieske Fe-S protein UQCRFS1
GO:0005739 mitochondrion
IEA
GO_REF:0000002
ACCEPT
Summary: InterPro2GO electronic annotation to the mitochondrion, based on the Complex1_LYR domain family. Correct but less specific than the matrix localisation.
Reason: Mitochondrial localisation is correct and well supported; this is simply a broader (parent) location than the experimentally established mitochondrial matrix. Retained as a valid, if general, CC annotation.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0005759 mitochondrial matrix
IEA
GO_REF:0000044
ACCEPT
Summary: Electronic annotation to the mitochondrial matrix from the UniProt Swiss-Prot subcellular location vocabulary mapping. Matches the curated UniProt location and experimental evidence.
Reason: Consistent with the experimentally determined (IDA, PMID:23168492) and curated UniProt matrix location where LYRM7 chaperones UQCRFS1.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0006457 protein folding
IEA
GO_REF:0000108
ACCEPT
Summary: Inter-ontology (logical) inference of a protein folding BP from the protein folding chaperone MF (GO:0044183). Consistent with LYRM7's role in stabilising/holding UQCRFS1.
Reason: This is a sound, if general, logical consequence of the chaperone MF. LYRM7 stabilises its unfolded/apo client UQCRFS1, which falls under protein folding. It is broader than the specific Complex III assembly BP but not incorrect. Kept as non-core context; the precise core BP is mitochondrial respiratory chain complex III assembly.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
stabilizing it prior to its translocation and insertion into the late
GO:0034551 mitochondrial respiratory chain complex III assembly
IEA
GO_REF:0000002
ACCEPT
Summary: InterPro2GO electronic annotation to Complex III assembly, based on the LYRM7-specific InterPro family (IPR045298). Correct and matches experimental evidence.
Reason: The LYRM7/MZM1-LYRM7 family signature reliably predicts a Complex III assembly-factor role, which is experimentally confirmed. This is the core BP.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
GO:0005515 protein binding
IPI
PMID:24606901
Cochaperone binding to LYR motifs confers specificity of iro...
MARK AS OVER ANNOTATED
Summary: IPI (IntAct) capturing a physical interaction between LYRM7 and HSC20/HSCB (UniProt Q8IWL3), the Fe-S cluster transfer cochaperone. This is a real and functionally meaningful interaction (LYRM7's LYR motif is an HSC20 binding site), but the GO term "protein binding" is uninformative.
Reason: Bare protein binding (GO:0005515) conveys no specific molecular function. The underlying LYRM7-HSC20 interaction is genuine and biologically important (it couples the UQCRFS1-LYRM7 intermediate to the Fe-S transfer machinery), so this is not removed; but the term is retained only as an uninformative over-annotation. The informative MF is the chaperone activity (GO:0044183).
Supporting Evidence:
PMID:24606901
SDHAF1 and LYRM7, respectively, are HSC20 binding partners
GO:0005515 protein binding
IPI
PMID:27499296
Mitochondrial Protein Interaction Mapping Identifies Regulat...
MARK AS OVER ANNOTATED
Summary: IPI (IntAct) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) reported in a large-scale mitochondrial protein interaction map. UQCRFS1 is the physiological client of LYRM7, so the interaction is correct, but "protein binding" is uninformative.
Reason: The LYRM7-UQCRFS1 interaction is the core, well-established relationship of this gene, but bare GO:0005515 does not capture the chaperone function. Retained as an uninformative over-annotation rather than removed.
Supporting Evidence:
PMID:27499296
Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
GO:0005515 protein binding
IPI
PMID:28380382
A Single Adaptable Cochaperone-Scaffold Complex Delivers Nas...
MARK AS OVER ANNOTATED
Summary: IPI (IntAct) capturing physical interactions of LYRM7 with UQCRFS1 (P47985) and with HSC20/HSCB (Q8IWL3). Both are physiologically central: the UQCRFS1-LYRM7 intermediate recruits HSC20 via LYRM7's LYR motif to deliver the [2Fe-2S] cluster to UQCRFS1.
Reason: The interactions are real and mechanistically important, but bare protein binding is uninformative and does not capture the chaperone/assembly-factor MF. Retained as an over-annotation rather than removed.
Supporting Evidence:
PMID:28380382
direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine) consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to the LYRM7-UQCRFS1 assembly intermediate
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome.
MARK AS OVER ANNOTATED
Summary: IPI from the HuRI binary (yeast two-hybrid) reference interactome mapping LYRM7 to SAT1 (P21673, spermidine/spermine N1-acetyltransferase). SAT1 has no known mitochondrial or Complex III role; this is most likely a non-physiological binary-screen hit.
Reason: Bare protein binding is uninformative, and this particular partner (SAT1) is not a plausible physiological interactor of a mitochondrial-matrix CIII assembly chaperone. Per curation policy, an experimental IPI is not removed on the basis of an incomplete assessment; it is marked as an uninformative (and here likely non-physiological) over-annotation.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome
GO:0005515 protein binding
IPI
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling...
MARK AS OVER ANNOTATED
Summary: IPI (BioPlex) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a proteome-scale affinity-purification interactome. Consistent with the core LYRM7-UQCRFS1 client relationship.
Reason: Correct interaction with the physiological client UQCRFS1, but bare GO:0005515 is uninformative. Retained as an over-annotation rather than removed; the chaperone MF (GO:0044183) captures the function.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human
GO:0005515 protein binding
IPI
PMID:40205054
Multimodal cell maps as a foundation for structural and func...
MARK AS OVER ANNOTATED
Summary: IPI capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a large-scale cell-map / structural-functional genomics interactome. Consistent with the core client relationship.
Reason: Correct interaction with UQCRFS1 but bare protein binding is uninformative. Retained as an over-annotation; the informative MF is the chaperone activity.
Supporting Evidence:
PMID:40205054
Multimodal cell maps as a foundation for structural and functional genomics
GO:0034551 mitochondrial respiratory chain complex III assembly
TAS
Reactome:R-HSA-9865881
ACCEPT
Summary: Reactome (TAS) annotation placing LYRM7 in the Complex III assembly pathway. Matches the core, experimentally supported BP.
Reason: Reactome curates LYRM7 as a Complex III assembly factor (the UQCRFS1/Rieske protein binds and is stabilised by LYRM7). This is the correct core BP.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
GO:0005739 mitochondrion
HTP
PMID:34800366
Quantitative high-confidence human mitochondrial proteome an...
ACCEPT
Summary: High-throughput annotation of LYRM7 to the mitochondrion from a quantitative high-confidence human mitochondrial proteome. Consistent with the curated matrix localisation.
Reason: Independent proteomic support for mitochondrial localisation; broader than the specific matrix location but correct.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0044183 protein folding chaperone
TAS
Reactome:R-HSA-9866253
ACCEPT
Summary: Reactome (TAS) assignment of the protein folding chaperone MF, corresponding to the reaction in which apo-UQCRFS1 binds and is stabilised by LYRM7. Matches the core chaperone function.
Reason: Reactome curates LYRM7 as the chaperone that binds and stabilises apo-UQCRFS1 in the matrix, the correct non-catalytic MF for this assembly factor. Core molecular function.
Supporting Evidence:
PMID:23168492
works as a human Rieske
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-9866253
ACCEPT
Summary: Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, the compartment where apo-UQCRFS1 binds LYRM7. Matches experimental and curated localisation.
Reason: Consistent with the experimentally established matrix location where LYRM7 chaperones UQCRFS1.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-9866272
ACCEPT
Summary: Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, associated with the reaction inserting the [2Fe-2S] cluster into UQCRFS1 as part of the UQCRFS1:LYRM7 complex.
Reason: Consistent with the matrix location where the LYRM7-UQCRFS1 intermediate recruits the Fe-S transfer machinery for cluster insertion.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0005515 protein binding
IPI
PMID:23168492
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step...
MARK AS OVER ANNOTATED
Summary: IPI (UniProt) capturing the physical interaction between LYRM7 and UQCRFS1 (P47985) from the primary characterisation paper, in which LYRM7 was shown to bind and stabilise the Rieske Fe-S protein. This is the defining, physiological interaction of LYRM7.
Reason: The LYRM7-UQCRFS1 interaction is the core relationship establishing LYRM7 as the UQCRFS1 chaperone, so it is not removed; however, bare protein binding (GO:0005515) is uninformative and does not capture the chaperone MF. The chaperone activity (GO:0044183) is the informative MF that should represent this function.
Supporting Evidence:
PMID:23168492
works as a human Rieske
GO:0005759 mitochondrial matrix
IDA
PMID:23168492
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step...
ACCEPT
Summary: Direct experimental (IDA) localisation of LYRM7 to the mitochondrial matrix from the primary characterisation study. This is the strongest evidence for the core localisation.
Reason: LYRM7 was experimentally shown to reside in and act within the mitochondrial matrix, where it binds and stabilises UQCRFS1. Core CC annotation.
Supporting Evidence:
PMID:23168492
binding to this subunit within the
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
GO:0031966 mitochondrial membrane
IDA
PMID:23168492
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step...
KEEP AS NON CORE
Summary: Direct experimental (IDA) detection of a pool of LYRM7 associated with the mitochondrial membrane, consistent with its transient association with the membrane-embedded late Complex III dimeric intermediate during UQCRFS1 insertion.
Reason: Membrane association is a real but secondary/transient aspect of LYRM7 function: its primary site of action is the matrix, where it chaperones UQCRFS1; the membrane pool reflects delivery of UQCRFS1 to the inner-membrane CIII intermediate. Kept but marked non-core relative to the matrix localisation.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
stabilizing it prior to its translocation and insertion into the late
GO:0034551 mitochondrial respiratory chain complex III assembly
IDA
PMID:23168492
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step...
ACCEPT
Summary: Direct experimental (IDA) evidence that LYRM7 is required for the UQCRFS1 insertion step of Complex III assembly. This is the definitive experimental support for the core BP.
Reason: The primary study established LYRM7 as a Complex III assembly factor acting at the UQCRFS1 incorporation step; this is the core, best-supported biological process.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
GO:0045333 cellular respiration
IDA
PMID:23168492
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step...
MARK AS OVER ANNOTATED
Summary: IDA annotation to cellular respiration, based on the observation that loss of LYRM7 impairs Complex III activity and hence respiration. LYRM7 is an assembly factor, not itself a respiratory-chain component; its effect on respiration is indirect (via enabling functional Complex III).
Reason: LYRM7 does not itself carry out or directly participate in respiration; it enables assembly of Complex III, whose activity is required for respiration. The precise, mechanistically accurate BP is mitochondrial respiratory chain complex III assembly (GO:0034551). Cellular respiration is an over-annotation capturing a downstream consequence rather than LYRM7's direct role. Not removed (experimental annotation) but flagged as over-annotated.
Supporting Evidence:
PMID:23168492
which enables formation of the mature and functional CIII

Core Functions

Non-catalytic protein-folding chaperone that binds and stabilises the Rieske iron-sulfur protein UQCRFS1 in the mitochondrial matrix, holding it prior to [2Fe-2S] cluster insertion and its incorporation into respiratory Complex III (cytochrome bc1). LYRM7's LYR motif also recruits the Fe-S transfer cochaperone HSC20, coupling the UQCRFS1-LYRM7 intermediate to the cluster-delivery machinery.

Supporting Evidence:
  • PMID:23168492
    works as a human Rieske
  • PMID:23168492
    LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
  • PMID:28380382
    direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine) consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to the LYRM7-UQCRFS1 assembly intermediate

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last steps of mitochondrial Complex III assembly in human cells.
Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster delivery.
Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.
A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur Clusters to Mammalian Respiratory Chain Complexes I-III.
A reference map of the human binary protein interactome.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
Multimodal cell maps as a foundation for structural and functional genomics.
Reactome:R-HSA-9865881
Complex III assembly
Reactome:R-HSA-9866253
apo-UQCRFS1 binds LYRM7
Reactome:R-HSA-9866272
2Fe-2S is inserted in UQCRFS1
file:human/LYRM7/LYRM7-uniprot.txt
UniProtKB entry Q5U5X0 (LYRM7_HUMAN)

Suggested Questions for Experts

Q: Does LYRM7 act purely as a holdase that stabilises apo-UQCRFS1, or does it also actively template/position UQCRFS1 for [2Fe-2S] cluster receipt and membrane insertion?

Suggested Experiments

Experiment: Reconstitute the UQCRFS1-LYRM7 intermediate with the HSC20-HSPA9-ISCU Fe-S transfer complex in vitro to determine the minimal components and the order of cluster insertion versus membrane insertion of UQCRFS1.

📚 Additional Documentation

Notes

(LYRM7-notes.md)

LYRM7 (Q5U5X0) review notes

Identity

  • Human LYRM7 = LYR motif-containing protein 7; synonyms C5orf31, MZM1L. HGNC:28072. 104 aa.
  • Ortholog of S. cerevisiae Mzm1 (SGD:S000002901; PANTHER PTN005318945). Complex I LYR family / MZM1-LYRM7 InterPro family (IPR045298, IPR050435; Pfam PF05347 Complex1_LYR).

Core function (verified)

  • Mitochondrial-matrix assembly chaperone for respiratory Complex III (cytochrome bc1 / ubiquinol-cytochrome c reductase). Non-catalytic.
  • Specifically a UQCRFS1 (Rieske Fe-S protein) chaperone: binds and stabilises UQCRFS1 in the mitochondrial matrix prior to its [2Fe-2S] cluster insertion, translocation and incorporation into the late CIII dimeric intermediate in the inner membrane.
  • PMID:23168492
  • PMID:23168492
  • LYR motif engages the Fe-S transfer cochaperone HSC20/HSCB (Q8IWL3): the UQCRFS1-LYRM7 intermediate recruits HSC20-HSPA9-ISCU to deliver the [2Fe-2S] cluster to UQCRFS1.
  • PMID:28380382
  • PMID:24606901

Localisation (verified)

  • Mitochondrial matrix (IDA, PMID:23168492; UniProt SUBCELLULAR LOCATION: Mitochondrion matrix). Also mitochondrial membrane (IDA, PMID:23168492 — consistent with association with the inner-membrane CIII intermediate). HTP mito proteome PMID:34800366.

Disease (context, not a GO annotation here)

  • Mitochondrial complex III deficiency, nuclear type 8 (MC3DN8; MIM:615838). Homozygous D25N impairs Rieske Fe-S incorporation into CIII; early-onset encephalopathy/leukoencephalopathy, lactic acidosis, severe CIII activity reduction. PMID:24014394.

GOA interactors (IPI WITH/FROM accessions)

  • P47985 = UQCRFS1 (Rieske) — the physiological client. Cited by PMID:23168492, 27499296, 28380382, 33961781, 40205054.
  • Q8IWL3 = HSCB/HSC20 — the Fe-S cochaperone. Cited by PMID:24606901, 28380382.
  • P21673 = SAT1 (diamine acetyltransferase) — from HuRI binary interactome (PMID:32296183); no known mitochondrial/CIII role; likely non-physiological Y2H hit.

GO term decisions

  • MF: GO:0044183 protein folding chaperone (IBA + Reactome TAS) is the correct non-catalytic MF. Keep as core. Do NOT invent a catalytic MF.
  • BP core: GO:0034551 mitochondrial respiratory chain complex III assembly (IDA/IBA/IEA/TAS) — accept as core.
  • CC: GO:0005759 mitochondrial matrix (IDA + IBA + IEA + TAS) core; GO:0005739 mitochondrion (IEA/HTP) broader-accept; GO:0031966 mitochondrial membrane (IDA) accept as non-core (association with membrane CIII intermediate).
  • GO:0006457 protein folding (IEA, inferred from the chaperone MF) — accept, general but sound.
  • GO:0045333 cellular respiration (IDA) — LYRM7 is an assembly factor, not itself part of respiration; the phenotype of its loss is impaired respiration. Mark as over-annotated (indirect; complex III assembly is the precise BP).
  • GO:0005515 protein binding IPIs — bare, uninformative MF; per policy MARK_AS_OVER_ANNOTATED (do not REMOVE). SAT1 hit noted as likely non-physiological but not removed.
  • Note: current CIII complex term is GO:0045275 (GO:0005750 obsolete); no complex-membership annotation is present in this GOA, and LYRM7 is a transient assembly factor, not a stable CIII subunit, so no in_complex is asserted.

📄 View Raw YAML

id: Q5U5X0
gene_symbol: LYRM7
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  LYRM7 (LYR motif-containing protein 7; also MZM1L/C5orf31) is a small mitochondrial-matrix
  LYR-family assembly chaperone for respiratory Complex III (cytochrome bc1 / ubiquinol-cytochrome
  c reductase). It acts as a dedicated chaperone for the Rieske iron-sulfur protein UQCRFS1,
  binding and stabilising UQCRFS1 in the mitochondrial matrix prior to insertion of its
  [2Fe-2S] cluster and the subunit's translocation and incorporation into the late Complex III
  dimeric intermediate in the inner membrane. Its LYR motif recruits the Fe-S transfer cochaperone
  HSC20 (HSCB), coupling the UQCRFS1-LYRM7 intermediate to the ISCU-HSPA9-HSC20 cluster-delivery
  machinery. LYRM7 is non-catalytic and is the human ortholog of yeast Mzm1. Loss-of-function
  variants cause mitochondrial complex III deficiency, nuclear type 8 (a leukoencephalopathy).
existing_annotations:
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) propagation placing LYRM7 in the mitochondrial matrix, where it acts
      as a chaperone. This is directly confirmed experimentally: LYRM7 binds and stabilises
      UQCRFS1 within the mitochondrial matrix.
    action: ACCEPT
    reason: >-
      The matrix location is the site of LYRM7's chaperone activity and is supported by direct
      experimental evidence (IDA, PMID:23168492) and the UniProt subcellular location, in
      addition to this phylogenetic inference. is_active_in is appropriate for the compartment
      where it chaperones UQCRFS1.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        binding to this subunit within the
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) inference that LYRM7 is involved in Complex III assembly. This is the
      core biological process of the gene and is strongly supported experimentally.
    action: ACCEPT
    reason: >-
      LYRM7 is a bona fide Complex III assembly factor mediating the UQCRFS1/Rieske Fe-S protein
      incorporation step. This is the precise, well-evidenced core BP and is consistent across
      IBA, IDA (PMID:23168492), IEA and Reactome TAS annotations.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) assignment of a protein folding chaperone molecular function. LYRM7
      is a non-catalytic chaperone that binds and stabilises (holds) its client UQCRFS1, so a
      chaperone MF is the correct, most informative non-catalytic molecular function.
    action: ACCEPT
    reason: >-
      The chaperone MF is directly supported: LYRM7 works as a UQCRFS1 chaperone, binding and
      stabilising the Rieske Fe-S protein prior to its incorporation into Complex III
      (PMID:23168492). This is the appropriate MF for this non-enzymatic assembly factor and is
      retained as the core molecular function; no catalytic activity should be assigned.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        works as a human Rieske
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: >-
        Assembly factor required for Rieske Fe-S protein UQCRFS1
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  review:
    summary: >-
      InterPro2GO electronic annotation to the mitochondrion, based on the Complex1_LYR domain
      family. Correct but less specific than the matrix localisation.
    action: ACCEPT
    reason: >-
      Mitochondrial localisation is correct and well supported; this is simply a broader (parent)
      location than the experimentally established mitochondrial matrix. Retained as a valid,
      if general, CC annotation.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation to the mitochondrial matrix from the UniProt Swiss-Prot subcellular
      location vocabulary mapping. Matches the curated UniProt location and experimental evidence.
    action: ACCEPT
    reason: >-
      Consistent with the experimentally determined (IDA, PMID:23168492) and curated UniProt
      matrix location where LYRM7 chaperones UQCRFS1.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  qualifier: involved_in
  review:
    summary: >-
      Inter-ontology (logical) inference of a protein folding BP from the protein folding
      chaperone MF (GO:0044183). Consistent with LYRM7's role in stabilising/holding UQCRFS1.
    action: ACCEPT
    reason: >-
      This is a sound, if general, logical consequence of the chaperone MF. LYRM7 stabilises its
      unfolded/apo client UQCRFS1, which falls under protein folding. It is broader than the
      specific Complex III assembly BP but not incorrect. Kept as non-core context; the precise
      core BP is mitochondrial respiratory chain complex III assembly.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: >-
        stabilizing it prior to its translocation and insertion into the late
- term:
    id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO electronic annotation to Complex III assembly, based on the LYRM7-specific
      InterPro family (IPR045298). Correct and matches experimental evidence.
    action: ACCEPT
    reason: >-
      The LYRM7/MZM1-LYRM7 family signature reliably predicts a Complex III assembly-factor role,
      which is experimentally confirmed. This is the core BP.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24606901
  qualifier: enables
  review:
    summary: >-
      IPI (IntAct) capturing a physical interaction between LYRM7 and HSC20/HSCB (UniProt Q8IWL3),
      the Fe-S cluster transfer cochaperone. This is a real and functionally meaningful interaction
      (LYRM7's LYR motif is an HSC20 binding site), but the GO term "protein binding" is
      uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare protein binding (GO:0005515) conveys no specific molecular function. The underlying
      LYRM7-HSC20 interaction is genuine and biologically important (it couples the UQCRFS1-LYRM7
      intermediate to the Fe-S transfer machinery), so this is not removed; but the term is
      retained only as an uninformative over-annotation. The informative MF is the chaperone
      activity (GO:0044183).
    supported_by:
    - reference_id: PMID:24606901
      supporting_text: >-
        SDHAF1 and LYRM7, respectively, are HSC20 binding partners
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27499296
  qualifier: enables
  review:
    summary: >-
      IPI (IntAct) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) reported in
      a large-scale mitochondrial protein interaction map. UQCRFS1 is the physiological client of
      LYRM7, so the interaction is correct, but "protein binding" is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The LYRM7-UQCRFS1 interaction is the core, well-established relationship of this gene, but
      bare GO:0005515 does not capture the chaperone function. Retained as an uninformative
      over-annotation rather than removed.
    supported_by:
    - reference_id: PMID:27499296
      supporting_text: Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28380382
  qualifier: enables
  review:
    summary: >-
      IPI (IntAct) capturing physical interactions of LYRM7 with UQCRFS1 (P47985) and with
      HSC20/HSCB (Q8IWL3). Both are physiologically central: the UQCRFS1-LYRM7 intermediate
      recruits HSC20 via LYRM7's LYR motif to deliver the [2Fe-2S] cluster to UQCRFS1.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interactions are real and mechanistically important, but bare protein binding is
      uninformative and does not capture the chaperone/assembly-factor MF. Retained as an
      over-annotation rather than removed.
    supported_by:
    - reference_id: PMID:28380382
      supporting_text: >-
        direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine)
        consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to
        the LYRM7-UQCRFS1 assembly intermediate
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      IPI from the HuRI binary (yeast two-hybrid) reference interactome mapping LYRM7 to SAT1
      (P21673, spermidine/spermine N1-acetyltransferase). SAT1 has no known mitochondrial or
      Complex III role; this is most likely a non-physiological binary-screen hit.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare protein binding is uninformative, and this particular partner (SAT1) is not a plausible
      physiological interactor of a mitochondrial-matrix CIII assembly chaperone. Per curation
      policy, an experimental IPI is not removed on the basis of an incomplete assessment; it is
      marked as an uninformative (and here likely non-physiological) over-annotation.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: A reference map of the human binary protein interactome
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  qualifier: enables
  review:
    summary: >-
      IPI (BioPlex) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a
      proteome-scale affinity-purification interactome. Consistent with the core LYRM7-UQCRFS1
      client relationship.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Correct interaction with the physiological client UQCRFS1, but bare GO:0005515 is
      uninformative. Retained as an over-annotation rather than removed; the chaperone MF
      (GO:0044183) captures the function.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: Dual proteome-scale networks reveal cell-specific remodeling of the human
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  qualifier: enables
  review:
    summary: >-
      IPI capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a large-scale
      cell-map / structural-functional genomics interactome. Consistent with the core client
      relationship.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Correct interaction with UQCRFS1 but bare protein binding is uninformative. Retained as an
      over-annotation; the informative MF is the chaperone activity.
    supported_by:
    - reference_id: PMID:40205054
      supporting_text: Multimodal cell maps as a foundation for structural and functional genomics
- term:
    id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9865881
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation placing LYRM7 in the Complex III assembly pathway. Matches the
      core, experimentally supported BP.
    action: ACCEPT
    reason: >-
      Reactome curates LYRM7 as a Complex III assembly factor (the UQCRFS1/Rieske protein binds
      and is stabilised by LYRM7). This is the correct core BP.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput annotation of LYRM7 to the mitochondrion from a quantitative high-confidence
      human mitochondrial proteome. Consistent with the curated matrix localisation.
    action: ACCEPT
    reason: >-
      Independent proteomic support for mitochondrial localisation; broader than the specific
      matrix location but correct.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9866253
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) assignment of the protein folding chaperone MF, corresponding to the reaction
      in which apo-UQCRFS1 binds and is stabilised by LYRM7. Matches the core chaperone function.
    action: ACCEPT
    reason: >-
      Reactome curates LYRM7 as the chaperone that binds and stabilises apo-UQCRFS1 in the matrix,
      the correct non-catalytic MF for this assembly factor. Core molecular function.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        works as a human Rieske
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9866253
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, the compartment where
      apo-UQCRFS1 binds LYRM7. Matches experimental and curated localisation.
    action: ACCEPT
    reason: >-
      Consistent with the experimentally established matrix location where LYRM7 chaperones
      UQCRFS1.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9866272
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, associated with the
      reaction inserting the [2Fe-2S] cluster into UQCRFS1 as part of the UQCRFS1:LYRM7 complex.
    action: ACCEPT
    reason: >-
      Consistent with the matrix location where the LYRM7-UQCRFS1 intermediate recruits the Fe-S
      transfer machinery for cluster insertion.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23168492
  qualifier: enables
  review:
    summary: >-
      IPI (UniProt) capturing the physical interaction between LYRM7 and UQCRFS1 (P47985) from the
      primary characterisation paper, in which LYRM7 was shown to bind and stabilise the Rieske
      Fe-S protein. This is the defining, physiological interaction of LYRM7.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The LYRM7-UQCRFS1 interaction is the core relationship establishing LYRM7 as the UQCRFS1
      chaperone, so it is not removed; however, bare protein binding (GO:0005515) is uninformative
      and does not capture the chaperone MF. The chaperone activity (GO:0044183) is the informative
      MF that should represent this function.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        works as a human Rieske
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IDA
  original_reference_id: PMID:23168492
  qualifier: located_in
  review:
    summary: >-
      Direct experimental (IDA) localisation of LYRM7 to the mitochondrial matrix from the primary
      characterisation study. This is the strongest evidence for the core localisation.
    action: ACCEPT
    reason: >-
      LYRM7 was experimentally shown to reside in and act within the mitochondrial matrix, where it
      binds and stabilises UQCRFS1. Core CC annotation.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        binding to this subunit within the
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
    id: GO:0031966
    label: mitochondrial membrane
  evidence_type: IDA
  original_reference_id: PMID:23168492
  qualifier: located_in
  review:
    summary: >-
      Direct experimental (IDA) detection of a pool of LYRM7 associated with the mitochondrial
      membrane, consistent with its transient association with the membrane-embedded late Complex
      III dimeric intermediate during UQCRFS1 insertion.
    action: KEEP_AS_NON_CORE
    reason: >-
      Membrane association is a real but secondary/transient aspect of LYRM7 function: its primary
      site of action is the matrix, where it chaperones UQCRFS1; the membrane pool reflects delivery
      of UQCRFS1 to the inner-membrane CIII intermediate. Kept but marked non-core relative to the
      matrix localisation.
    supported_by:
    - reference_id: file:human/LYRM7/LYRM7-uniprot.txt
      supporting_text: >-
        stabilizing it prior to its translocation and insertion into the late
- term:
    id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  evidence_type: IDA
  original_reference_id: PMID:23168492
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental (IDA) evidence that LYRM7 is required for the UQCRFS1 insertion step of
      Complex III assembly. This is the definitive experimental support for the core BP.
    action: ACCEPT
    reason: >-
      The primary study established LYRM7 as a Complex III assembly factor acting at the UQCRFS1
      incorporation step; this is the core, best-supported biological process.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
    id: GO:0045333
    label: cellular respiration
  evidence_type: IDA
  original_reference_id: PMID:23168492
  qualifier: involved_in
  review:
    summary: >-
      IDA annotation to cellular respiration, based on the observation that loss of LYRM7 impairs
      Complex III activity and hence respiration. LYRM7 is an assembly factor, not itself a
      respiratory-chain component; its effect on respiration is indirect (via enabling functional
      Complex III).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      LYRM7 does not itself carry out or directly participate in respiration; it enables assembly
      of Complex III, whose activity is required for respiration. The precise, mechanistically
      accurate BP is mitochondrial respiratory chain complex III assembly (GO:0034551). Cellular
      respiration is an over-annotation capturing a downstream consequence rather than LYRM7's
      direct role. Not removed (experimental annotation) but flagged as over-annotated.
    supported_by:
    - reference_id: PMID:23168492
      supporting_text: >-
        which enables formation of the mature and functional CIII
core_functions:
- description: >-
    Non-catalytic protein-folding chaperone that binds and stabilises the Rieske iron-sulfur
    protein UQCRFS1 in the mitochondrial matrix, holding it prior to [2Fe-2S] cluster insertion
    and its incorporation into respiratory Complex III (cytochrome bc1). LYRM7's LYR motif also
    recruits the Fe-S transfer cochaperone HSC20, coupling the UQCRFS1-LYRM7 intermediate to the
    cluster-delivery machinery.
  molecular_function:
    id: GO:0044183
    label: protein folding chaperone
  directly_involved_in:
  - id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:23168492
    supporting_text: >-
      works as a human Rieske
  - reference_id: PMID:23168492
    supporting_text: >-
      LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
  - reference_id: PMID:28380382
    supporting_text: >-
      direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine)
      consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to
      the LYRM7-UQCRFS1 assembly intermediate
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: PMID:23168492
  title: LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last steps of mitochondrial
    Complex III assembly in human cells.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary characterisation of human LYRM7/MZM1L. Establishes it as a mitochondrial-matrix
      UQCRFS1 (Rieske Fe-S) chaperone and Complex III assembly factor. Supports the core MF, BP,
      and matrix localisation.
- id: PMID:24606901
  title: Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster
    delivery.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text explicitly names LYRM7 as an HSC20 (HSC20/HSCB) binding partner among the LYR-motif
      family that assist Complex II/III assembly, supporting the LYRM7-HSC20 interaction.
- id: PMID:27499296
  title: Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
    Chain Function.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Large-scale mitochondrial interaction map; source of an IntAct LYRM7-UQCRFS1 interaction.
      Supports the physiological client relationship but not gene-specific mechanism.
- id: PMID:28380382
  title: A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur
    Clusters to Mammalian Respiratory Chain Complexes I-III.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text details the UQCRFS1-LYRM7 intermediate recruiting HSC20 via LYRM7's LYR motif to
      deliver the [2Fe-2S] cluster to UQCRFS1. Strong mechanistic support for the core function.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      HuRI binary (Y2H) interactome; source of an IntAct LYRM7-SAT1 hit. SAT1 has no known
      mitochondrial/CIII role, so this is likely a non-physiological binary-screen interaction.
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      BioPlex proteome-scale interactome; source of an IntAct LYRM7-UQCRFS1 interaction consistent
      with the core client relationship.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      High-confidence mitochondrial proteome; supports mitochondrial localisation of LYRM7 (HTP).
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Large-scale cell-map interactome; source of an IntAct LYRM7-UQCRFS1 interaction consistent
      with the core client relationship.
- id: Reactome:R-HSA-9865881
  title: Complex III assembly
  findings: []
- id: Reactome:R-HSA-9866253
  title: apo-UQCRFS1 binds LYRM7
  findings: []
- id: Reactome:R-HSA-9866272
  title: 2Fe-2S is inserted in UQCRFS1
  findings: []
- id: file:human/LYRM7/LYRM7-uniprot.txt
  title: UniProtKB entry Q5U5X0 (LYRM7_HUMAN)
  findings: []
suggested_questions:
- question: >-
    Does LYRM7 act purely as a holdase that stabilises apo-UQCRFS1, or does it also
    actively template/position UQCRFS1 for [2Fe-2S] cluster receipt and membrane insertion?
suggested_experiments:
- description: >-
    Reconstitute the UQCRFS1-LYRM7 intermediate with the HSC20-HSPA9-ISCU Fe-S transfer complex
    in vitro to determine the minimal components and the order of cluster insertion versus
    membrane insertion of UQCRFS1.