Human CD79A (P11912) was absent from GitHub main at the initial check (main d763bc99e4aee5c0df05fd45468e96c1da033ef9); an open-PR search for CD79A returned no matches. The normal fetch-gene human CD79A command ran against an isolated copy of the current, unmodified repository code and produced a fresh UniProt record, GOA table and seed with 206 assertions, two alternative products and 23 references. The original normal outputs are preserved in the working archive.
For publications and Reactome, existing canonical bytes were selected where available. Freshly downloaded variants were preserved separately rather than replacing canonical caches. No source publication, GOA or UniProt content was edited. Normal family-data outputs remain in the intake archive and are not used to assert a new PANTHER family classification. Research and source selection were performed in an isolated working directory before publication.
The genuine Falcon attempt timed out after 90 seconds. The explicit perplexity-lite fallback then failed after repeated dependency-download attempts; no provider report was produced. Manual primary research continued. The normal publication-caching command reused all seven original PMID caches. Four additional references were obtained through the normal fetch command: PMIDs 10525050, 7643857, 8617796 and 10900006.
CD79A is the Ig-alpha component of the CD79A/CD79B signaling heterodimer. The human IgM-BCR structure directly places this heterodimer alongside the membrane immunoglobulin heavy and light chains. The heterodimer contributes assembly and signal transmission; immunoglobulin provides antigen recognition. CD79A's cytoplasmic ITAM is phosphorylated by kinases and supplies docking sites for signaling proteins, rather than performing kinase chemistry itself. PMID:35981043(https://pubmed.ncbi.nlm.nih.gov/35981043/), Reactome:R-HSA-983700.
Human surface-expression experiments support the requirement for intact receptor assembly. The study includes tonsillar B cells and lymphoma cell lines; loss of CD79A or CD79B removes surface IgM, while consequences for fitness differ among models. Its surface-staining methods were accessible beyond the abstract. This should not become a universal claim that every CD79A-deficient cell dies immediately. PMID:36426942(https://pubmed.ncbi.nlm.nih.gov/36426942/).
The human agammaglobulinemia study identifies a splice defect disrupting the membrane receptor subunit and a block at the pro-B to pre-B transition. It explicitly distinguishes this checkpoint from immunoglobulin gene rearrangement. Thus, the existing differentiation annotations fit CD79A's receptor role; no recombinase function is inferred. PMID:10525050(https://pubmed.ncbi.nlm.nih.gov/10525050/).
Cytoplasmic-tail experiments support cooperative signaling by Ig-alpha/Ig-beta, but their assay context matters: PMID:8617796 uses PDGFR-tail chimeras in a murine B-cell line. The phosphorylation-regulation study supplies additional mechanistic background, without establishing every residue-specific event in endogenous human B cells. PMID:8617796(https://pubmed.ncbi.nlm.nih.gov/8617796/), PMID:10900006(https://pubmed.ncbi.nlm.nih.gov/10900006/).
These are one coherent core unit: a signaling and assembly subunit contributing to transmembrane receptor activity in the BCR complex. The source IBA and ISS receptor rows already use contributes_to. The IEA row has enables; that machine field is preserved, while its reason and the core synthesis explicitly state the complex-subunit interpretation. No separate autonomous antigen-receptor or enzymatic activity is assigned.
Both source products are preserved: P11912-1 (long) and P11912-2 (short). The UniProt source maps the short product to an extracellular sequence alteration, and the original splice study detects variant transcripts in human B cells. The accessible study does not establish that the short product is a stable functional receptor subunit. Retaining the two source records therefore does not imply equivalent surface assembly, signaling or physiological abundance. PMID:7643857(https://pubmed.ncbi.nlm.nih.gov/7643857/).
No residue-specific function was inferred for the short product merely from retention of the cytoplasmic tail. The proposed experiment first establishes protein expression and then compares assembly and signaling in a controlled human B-cell setting.
All 206 source assertions retain their original term, qualifier, evidence, reference and partner/product fields. Decisions are 33 ACCEPT, 172 KEEP_AS_NON_CORE and one MODIFY. There are no NEW, REMOVE, UNDECIDED or PENDING decisions. The single MODIFY refines the general cell-surface signaling pathway to B-cell receptor signaling. No new process is proposed.
Plasma-membrane and receptor-complex assignments are supported by human structure and surface-expression evidence. The external-side IBA uses is_active_in: extracellular CD79A contacts membrane immunoglobulin and contributes to receptor assembly there, while ITAM signaling occurs on the cytoplasmic side. This structural contribution does not assign autonomous antigen binding to CD79A. The broad membrane term and conditional raft/endocytic locations are retained as non-core. The multivesicular-body and raft annotations preserve their orthology provenance; this review does not claim newly inspected human imaging experiments for those transfers. Signal transmission is not restricted to rafts.
The isolated Ig-alpha cytoplasmic domain can oligomerize in vitro according to the original abstract. The identical-protein-binding annotation is therefore retained as non-core; this does not replace the physiological CD79A/CD79B heterodimer with a CD79A homodimer. The title foregrounding T-cell receptor zeta is not a reason to reject explicitly reported Ig-alpha assays. PMID:14967045(https://pubmed.ncbi.nlm.nih.gov/14967045/).
The Fc-mu-receptor structural paper discusses IgM-BCR context, but its abstract does not enumerate every BCR subunit. The exact CD79A inclusion in that paper was not independently inspected. The IgM-complex annotation remains accepted because it is directly established by the independent human BCR structure; no misattribution claim is made from the Fc-mu-receptor-focused title. PMID:36949194(https://pubmed.ncbi.nlm.nih.gov/36949194/), PMID:35981043(https://pubmed.ncbi.nlm.nih.gov/35981043/).
PAINT assertions are evaluated against inherited receptor biology, not donor counts. CD79A's presence among descendant evidence for the BCR complex is legitimate and is not treated as circular. The ancestral node placement and complete electronic/orthology chains were not independently rebuilt.
A separate reviewer checked all 166 source screen assertions against exact source-specific target records. The evidence and limitations are summarized below. The public IntAct target query and author U2OS network identify the underlying records.
All these interactions remain KEEP_AS_NON_CORE under the project's explicit instruction to retain supported correct generic binding when a more informative activity is not established. No screened partner's biochemical function is transferred to CD79A. The 166 resulting generic-binding warnings are understood and intentional. Partner isoform identifiers describe the curated/tested product and do not, by themselves, establish isoform-exclusive binding.
All eleven publication abstracts were read. The human disease paper's accessible PMC HTML includes the methods, patient/mutation results, differentiation data and discussion inspected here. The structural and splice papers, domain-oligomerization paper and tail-function papers remain abstract-only for this review. For PMID:36426942, selected accessible main text through the methods supplemented its immutable abstract-only cache; a subsequent web retrieval returned a browser challenge, and an independent Europe PMC XML request returned HTTP 500. No complete main-text or figure-pixel read is claimed.
The screen reports were assessed through their accessible abstracts, relevant method context and the independent exact-target consultation. Cached HTML being flagged available does not establish that a complete original paper or every supplementary table was inspected. Reference assessments distinguish positive identity/record checks from such limitations. No unavailable source was silently replaced by a generated provider narrative.
All ten existing Reactome summaries were read. They locate the BCR-associated assembly and assign catalysis to the appropriate named kinases, phosphatase or phospholipase. No drug-target, therapeutic or catalytic activity is inherited by CD79A merely from participation in those cached events. No new process is inferred from the absence of CD79A/P11912 in the cached GO-CAM index search.
Normal schema/reference/GO-term validation, status checking and rendering use unmodified repository code and authentic source caches in the isolated workspace. The 166 warnings concern the supported generic-binding rows retained by explicit policy. DRAFT is the normal derived status in the presence of these warnings; it does not mean any source assertion remains PENDING.
Structural comparison confirms preservation of all 206 original assertions outside their review blocks and both alternative products. Two short verbatim anchors appear once each in the YAML; these notes include no source quotations. The audit verifies exact cache substrings and aggregate per-source word counts including repetitions. Independent review checked the annotation decisions, exact interaction evidence and selected primary disease and structural results before publication. Source caches remain unchanged; curation history accompanies the review.
CD79A couples the antigen-recognition module to cytoplasmic signaling by providing a physical receptor-associated platform for signaling proteins. The phosphorylated ITAM recruits SYK. A separate phosphorylated site outside the ITAM recruits BLNK, positioning this adaptor to link receptor-proximal kinase activity to downstream pathways. The direct recruitment study reports that "BLNK bound directly to phospho-Y204" and that fusion of BLNK to a mutant Ig-alpha tail restored downstream signaling. The site number is the study's numbering; the human UniProt record identifies the corresponding BLNK site as Tyr210 by similarity. These are distinct docking sites, and the non-ITAM BLNK experiment is not recast as an ITAM-binding assay. PMID:11909947(https://pubmed.ncbi.nlm.nih.gov/11909947/), Reactome:R-HSA-983700.
The BLNK study was assessed from its primary abstract; its full Methods were not accessible, so construct/cell species is not independently established here. A separate biochemical study directly tests CD79A phospho-ITAM binding to purified human SYK tandem-SH2 domains. The selected Results and Methods include target-specific TR-FRET and phosphopeptide competition, with nonphosphorylated controls. This supports the ITAM docking arm. CD79A was part of the binding panel, not one of the three solved phosphopeptide structures, and these purified components are distinct from native-cell signaling measurements. PMID:39442513(https://pubmed.ncbi.nlm.nih.gov/39442513/).
This mechanism supports signaling receptor complex adaptor activity, GO:0030159, alongside the existing contribution to transmembrane signaling receptor activity in the same core unit. The current GO definition describes physical support for assembly of a receptor signaling complex. The assignment rests on CD79A recruitment evidence; the analogous CD3G/CD247 annotations are useful consistency checks but do not supply evidence for this protein. No new annotation row or process is added, and no kinase catalysis is assigned to CD79A.
B-cell proliferation is retained as a non-core cellular outcome in both existing orthology-derived rows. Its dependence on signaling context and cell state distinguishes it from the defining receptor/adaptor mechanism. Human CD79A/CD79B loss experiments show loss of surface IgM across the tested cell lines, with fitness effects in only a subset; fitness combines growth and survival and does not itself identify the mechanism of cell division. The original evidence codes, mouse supporting entities and source references are preserved. PMID:36426942(https://pubmed.ncbi.nlm.nih.gov/36426942/).
The external-side PAINT assertion concerns the extracellular interface through which CD79A contributes to the assembled receptor. The ITAM and non-ITAM adaptor sites act on the cytoplasmic side. These functions occupy different parts of a transmembrane subunit; the external-side statement does not relocate cytoplasmic docking. The biological description now states the short transcript's extracellular deletion without curation commentary, while the alternative-product limitations and proposed expression/function tests above remain applicable. PMID:35981043(https://pubmed.ncbi.nlm.nih.gov/35981043/), PMID:7643857(https://pubmed.ncbi.nlm.nih.gov/7643857/).
This dated follow-up supersedes the earlier action counts and absence of a notes quotation. The current 206 decisions are 31 ACCEPT, 174 KEEP_AS_NON_CORE and one MODIFY. All source assertion fields and both alternative products remain exact. The new short primary anchor is included in the aggregate per-source quotation audit. Screen evidence and partner accessions retain their prior exact-source audit; no unverified symbol substitutions were introduced.
All rows were reconsidered against the existing source-specific review, UniProt and primary caches. Current generic-binding policy replaces the older explicit NONCORE retention rule; interaction payloads and prior provenance remain intact. Broad membrane is refined to plasma membrane. Extracellular-side rationales now depend on topology and assembly rather than an ordinary relationship qualifier. CD79A multivesicular-body inference is anchored to direct mouse Fig. 5C immunogold (PMID11854359); CD79B developmental participation is supported by human disease and comparative mouse loss-of-function (PMIDs17675462/12097390). Purified domain self-association (PMIDs14967045/20696394) remains distinct from physiological receptor stoichiometry. Full 2022 Science structural texts could not be recovered after normal refresh/publisher attempts; their abstracts directly establish human IgM-BCR composition. Other original source-access limitations remain explicit rather than relabeled as newly read full text.
All original annotation payloads, evidence codes, supporting entities, relationship fields and flags are preserved. Review decisions judge biological claims; ordinary relationship qualifiers are not used to change their meaning. No new annotation rows were proposed. Actual Falcon and perplexity-lite attempts failed authentication/quota; manual source inspection is documented here instead of a fabricated provider report. The existing PIK3R1 provider report was reused as discovery, with primary evidence assessed separately.
All three receptor-activity rows receive the same lateral adaptor-role clarification, grounded in human SYK/CD79A phosphopeptide binding (PMID39442513) and separate BLNK docking evidence (PMID11909947). Ordinary relationship qualifiers did not determine the action; no source_defects qualifier correction was invented. CD79B retains its supported receptor-complex contribution. Bare UniProt location citations are replaced by actual relevant CC text, or removed when native ortholog microscopy already supplies the evidence; no fabricated multivesicular-body quote.
The committed PTHR14334 PAINT slice explicitly places GO:0004888 at PTN000371571 with MGI:MGI:101774 grounding. This inherited receptor-complex contribution is not a propagation failure; structured metadata records NO_FAILURE_CORE. The target-level adaptor refinement does not claim that the ancestral placement, donor number or complex contribution is wrong.
Restored the two GO:0004888 contributes_to annotations (IBA and ISS) to ACCEPT. The annotation-reviewer policy explicitly treats contributes_to as a meaningful weaker complex-subunit claim; ordinary relationship metadata remains inert. Human IgM-BCR composition (PMID:35981043, cached abstract), human CD79A/CD79B assembly experiments (PMID:36426942, cached abstract and previously documented limited full-text access), and direct phospho-ITAM docking (full PMID:39442513) support this structural/signaling contribution. The IEA row remains MODIFY to GO:0030159 on adaptor biology, not on its ordinary relationship field. The PAINT node PTN000371571 retains NO_FAILURE_CORE. The original ISS identifier is preserved without claiming an unverified donor identity. Replaced the incomplete PMID:39442513 quotation with its complete sentence, including the citation parenthetical. Core functions and all machine payloads are unchanged.
Focused validation reports no errors but emits an action-consistency warning because it groups the qualified contribution annotations with the remaining receptor-activity row. The explicit contributes_to policy exception justifies this difference; the actions are not being changed to suppress the warning. No validator or policy configuration is modified.