id: A0A494B8X4 gene_symbol: Sdhaf2 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:10090 label: Mus musculus description: >- Sdhaf2 (succinate dehydrogenase complex assembly factor 2; SDH5/Sdh5/SdhE family, PANTHER PTHR12469:SF2) is a nuclear-encoded mitochondrial matrix protein that binds the flavoprotein subunit SDHA of respiratory complex II and, acting as a dedicated chaperone-like assembly factor rather than an enzyme, promotes covalent attachment of FAD to SDHA and thereby assembly of active succinate dehydrogenase. The canonical mouse product is Q8C6I2 (164 aa). A0A494B8X4 is a 135-residue alternative product of the same gene (Ensembl ENSMUSP00000157391) that is identical to the canonical protein over residues 1-121, including the mitochondrial transit peptide, the N-terminal helical bundle and the glycine equivalent to human Gly78 that is needed for SDHA binding, but replaces canonical residues 122-164 with an unrelated 14-residue tail. It therefore lacks the C-terminal part of the Sdh5 domain (Pfam PF03937 66-141 in the canonical product, 66-124 here), including the helix corresponding to human residues 135-145 and the C-terminal helical segment. It is expected to be imported into mitochondria; whether it folds, binds SDHA or supports flavinylation has not been tested. existing_annotations: - term: id: GO:0005759 label: mitochondrial matrix evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0170 review: action: ACCEPT summary: >- Matrix localization is well grounded for the gene product. The eukaryotic PAINT node PTN000279729 of PTHR12469, which contains this mouse product through subfamily SF2, carries an IBD for mitochondrion (GO:0005739) seeded by yeast Sdh5, human SDHAF2 and Arabidopsis SDHAF2. SDHAF2 acts on SDHA, a matrix-facing protein, and A0A494B8X4 keeps the complete 27-residue mouse transit peptide, identical to the canonical Q8C6I2. The UniProt SubCell line behind this row is itself an ARBA prediction, so it is not quoted here. Mitochondrial matrix is as precise as the evidence allows and is the most confidently transferable property of this alternative product. reason: >- Accepted on the basis of the retained targeting peptide (re-review structural mapping) and the PAINT eukaryotic-node placement; no product-specific localization assay exists. supported_by: - reference_id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md supporting_text: '| Mitochondrial transit peptide | 1-29 | Yes (mouse 1-27, identical to Q8C6I2) |' - reference_id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS.md supporting_text: '| Transit peptide: Mitochondrion | 1–27 | 27 / 27 | 27 |' - reference_id: PMID:19628817 supporting_text: we investigated an uncharacterized but highly conserved mitochondrial protein (named here Sdh5) - term: id: GO:0010719 label: negative regulation of epithelial to mesenchymal transition evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00085215 review: action: MARK_AS_OVER_ANNOTATED summary: >- ARBA association rule echoing a single lung-cancer study (PMID:23983127) in which loss of SDH5 was followed by EMT marker changes in cell lines, tumour specimens and SDH5 knockout mouse lung epithelium. That is a downstream cellular phenotype of losing a mitochondrial complex II assembly factor, not evidence that the protein performs a step in regulating EMT. PAINT curators placed mitochondrial, complex II assembly, TCA-cycle and succinate-to-ubiquinone electron-transport terms on the eukaryotic node PTN000279729 and did not propagate EMT or Wnt regulation, which is read as a deliberate decision. For this alternative product, which lacks the C-terminal part of the Sdh5 domain and was never assayed, the involved_in claim is an over-annotation. reason: >- Knockout/knockdown phenotype (necessity) does not establish participation; electronic ARBA transfer to a truncated alternative product with no phylogenetic support for the term. The experimentally based gene-level association, if any, belongs on the canonical product with an acts_upstream_of_or_within qualifier. supported_by: - reference_id: PMID:23983127 supporting_text: In SDH5 knock-out mice, lung epithelial cells exhibited elevated mesenchymal markers, which is characteristic of EMT. - reference_id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md supporting_text: '| Helix 135-145 | | No: aligned positions are the unrelated tail (2/11 identical) |' - term: id: GO:0090090 label: negative regulation of canonical Wnt signaling pathway evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027950 review: action: MARK_AS_OVER_ANNOTATED summary: >- ARBA association rule derived from the same lung-cancer study (PMID:23983127), which reported that SDH5 modulates GSK-3-beta/beta-catenin signalling in human lung-cancer cells. The claim rests on one cell-context study and has not been placed by PAINT on any PTHR12469 node, whereas the conserved, structurally characterised role of the family is SDHA flavinylation inside mitochondria. A cytosolic Wnt-regulatory activity for a matrix-targeted assembly factor is not established, and nothing is known about it for the C-terminally altered A0A494B8X4 product. Over-annotation for this product. reason: >- Single context-dependent study, no phylogenetic support (absent from PAINT IBD set), and the target is an unassayed alternative product lacking part of the Sdh5 domain. supported_by: - reference_id: PMID:23983127 supporting_text: SDH5 functions as a negative regulator of Wnt-β-catenin signaling. references: - 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:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: PMID:38569044 title: Drp1 controls complex II assembly and skeletal muscle metabolism by Sdhaf2 action on mitochondria. findings: - statement: Mouse muscle and myocyte experiments connect mitochondrial Sdhaf2 availability to complex-II assembly and activity; they do not isolate the 135-residue alternative product. supporting_text: 'Restoration of Sdhaf2 normalized complex II activity, lipid oxidation, and insulin action in Drp1-KD myocytes.' full_text_unavailable: false reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Primary mouse study checked against the cached text. Supports the gene-level complex II role of Sdhaf2 (canonical product); it does not assay A0A494B8X4, so in the 2026-10-21 re-review it is no longer cited as support for the matrix-localization row of this alternative product and is retained as gene-level context. - id: PMID:23983127 title: Succinate dehydrogenase 5 (SDH5) regulates glycogen synthase kinase 3β-β-catenin-mediated lung cancer metastasis. findings: - statement: The study reports an EMT-marker phenotype in SDH5 knockout mouse lung epithelium, i.e. a loss-of-function (necessity) phenotype rather than evidence of participation in EMT regulation. supporting_text: In SDH5 knock-out mice, lung epithelial cells exhibited elevated mesenchymal markers, which is characteristic of EMT. - statement: Human lung-cell experiments link SDH5 to GSK3-beta/beta-catenin regulation in a context-dependent mechanism, rather than establishing a universal Wnt effect of all products. supporting_text: SDH5 functions as a negative regulator of Wnt-β-catenin signaling. full_text_unavailable: false reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Primary report checked against the cached full text. Single cancer-context study; the EMT and Wnt findings are downstream/context-dependent and were not propagated by PAINT for the PTHR12469 family. None of the experiments uses the A0A494B8X4 product. - id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS.md title: Exact Sdhaf2 product and mitochondrial-targeting sequence comparison reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Re-read the reproducible same-gene sequence comparison; it supports retaining the mitochondrial-targeting evidence while warning that the short exact product cannot be assumed to perform every full-length SDHAF2 function. - id: file:mouse/Sdhaf2/Sdhaf2-protnlm-source.json title: Frozen exact-input ProtNLM output and UniProt sequence for A0A494B8X4 reference_review: relevance: NONE review_notes: >- Not used as evidence in the 2026-10-21 re-review, which was performed independently of ProtNLM2 output. Retained in the list only for provenance of the earlier review. - id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md title: Sdhaf2 re-review structural-feature mapping of A0A494B8X4 reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Reproducible mapping (map_structure_rereview.py, live UniProt/InterPro inputs) of human SDHAF2 PDB-derived helices, the Gly78 disease residue and the transit peptide onto the canonical and alternative mouse products. - id: PMID:19628817 title: SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Founding yeast/human study (abstract cached); establishes Sdh5 as a conserved mitochondrial protein that binds the SDH flavoprotein and is required for its flavination. Yeast Sdh5 (SGD:S000005432) is a seed of the PAINT eukaryotic node. - id: PMID:32887801 title: The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Human SDHA-SDHAF2 biochemistry/structure (abstract cached); supports the chaperone-like role of SDHAF2 in orienting SDHA domains for covalent flavinylation. - id: file:interpro/panther/PTHR12469/PTHR12469-paint.tsv title: PAINT IBD/IRD assertions for PANTHER PTHR12469 reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Eukaryotic node PTN000279729 carries IBDs for GO:0005739, GO:0006099, GO:0006121 and GO:0034553 (seeds include yeast Sdh5 and human SDHAF2 Q9NX18); no EMT, Wnt or protein-FAD linkage term is propagated. core_functions: - description: >- Gene-level function of Sdhaf2, inherited from the PTHR12469 eukaryotic node PTN000279729: a mitochondrial matrix assembly factor that binds SDHA and licenses covalent FAD attachment for complex II assembly. For the A0A494B8X4 alternative product only mitochondrial (matrix) targeting is confidently retained; the molecular activity is not asserted here because the product lacks the C-terminal part of the Sdh5 domain and has not been assayed. locations: - id: GO:0005759 label: mitochondrial matrix supported_by: - reference_id: PMID:19628817 supporting_text: Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination - reference_id: PMID:32887801 supporting_text: works in synergy with SDHAF2 to properly orient the flavin and - reference_id: file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md supporting_text: The product keeps the targeting peptide, the N-terminal helical bundle and the RGxxE knowledge_gaps: - gap_statement: >- Whether the 135-residue A0A494B8X4 product is translated in vivo, folds without the C-terminal helices of the Sdh5 domain, and binds SDHA or supports its flavinylation is unknown. gap_kind: - BIOLOGY suggested_questions: - question: Does the 135-residue mouse product bind SDHA and promote covalent FAD attachment after mitochondrial import? - question: >- Is the GSK-3-beta/beta-catenin effect of SDH5 loss (PMID:23983127) a direct activity of SDHAF2 or a secondary consequence of complex II deficiency (e.g. succinate accumulation)? suggested_experiments: - description: >- Express A0A494B8X4 and the canonical Q8C6I2 in Sdhaf2-null mouse cells and compare mitochondrial import, co-immunoprecipitation with SDHA, covalent flavin content of SDHA (in-gel flavin fluorescence) and complex II activity.