Is BAIAP3 p.Met1069Val (c.3205A>G) pathogenic?

BAIAP3 p.Met1069Val (c.3205A>G) is classified Uncertain significance in BAIAP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-24). AlphaMissense: ambiguous (0.4973); Very rare (popmax 0.0022%, sas).

How common is BAIAP3 p.Met1069Val (c.3205A>G) in the general population?

BAIAP3 p.Met1069Val (c.3205A>G) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about BAIAP3 p.Met1069Val (c.3205A>G)?

AlphaMissense predicts ambiguous (score 0.4973) — an in-silico prediction, not a clinical call.

BAIAP3 p.Met1069Val

c.3205A>G · rs766371544 · VCV3132921

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4973 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Computational evidence

Protein change
AlphaMissense	0.4973	ambiguous
REVEL	0.611	indeterminate
SaProt	LLR -9.89	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.1	GERP -1.2, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 9,929 bp · p 2.6e-07 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM M1104V vs ClinVar M1069V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,076 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000343% 5/1,455,718 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,538
European (non-Finnish)	0.000254%	393,249

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.Met1069Val
Coding: c.3205A>G
MANE Select: NM_001199097
dbSNP: rs766371544
Type: single nucleotide variant
Location: chr16:1348151 (GRCh38)
Gene constraint: LOEUF 1.406 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.27
Residue 1069: the c2 2 domain

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-met1069val (accessed [today's date]).

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