Is BAIAP3 p.Cys519Tyr (c.1556G>A) pathogenic?

BAIAP3 p.Cys519Tyr (c.1556G>A) is classified Uncertain significance in BAIAP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-07). AlphaMissense: likely benign (0.1834); Very rare (popmax 0.01%, amr).

How common is BAIAP3 p.Cys519Tyr (c.1556G>A) in the general population?

BAIAP3 p.Cys519Tyr (c.1556G>A) is very rare (popmax 0.01%, amr) (gnomAD).

What do computational predictors say about BAIAP3 p.Cys519Tyr (c.1556G>A)?

AlphaMissense predicts likely benign (score 0.1834) — an in-silico prediction, not a clinical call.

BAIAP3 p.Cys519Tyr

c.1556G>A · rs767326712 · VCV3132898

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1834 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.01%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1834	likely benign
REVEL	0.514	indeterminate
SaProt	LLR -7.36	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 9,929 bp · p 2.6e-07 · regional, not allelic
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM C554Y vs ClinVar C519Y) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/60,010 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.00335% 54/1,613,756 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	10,002
European (non-Finnish)	0.00407%	24,584

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BAIAP3
Protein: p.Cys519Tyr
Coding: c.1556G>A
MANE Select: NM_001199097
dbSNP: rs767326712
Type: single nucleotide variant
Location: chr16:1344271 (GRCh38)
Gene constraint: LOEUF 1.406 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.27

Full BAIAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAIAP3 c.-11+926G>T Uncertain significance ★ ⚠ same type
BAIAP3 c.-11+983T>A Uncertain significance ★ ⚠ same type
BAIAP3 c.-11+985G>A Uncertain significance ★ ⚠ same type
BAIAP3 c.-11+991G>A Uncertain significance ★ ⚠ same type
BAIAP3 c.-11+996C>G Uncertain significance ★ ⚠ same type
BAIAP3 c.-6C>T Uncertain significance ★ ⚠ same type
BAIAP3 p.Ala1007Gly Uncertain significance ★ ⚠ same type
BAIAP3 p.Ala1056Val Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/baiap3-p-cys519tyr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown