Is BAIAP2 p.Met79Val (c.235A>G) pathogenic?

BAIAP2 p.Met79Val (c.235A>G) is classified Uncertain significance in BAIAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-22). AlphaMissense: likely pathogenic (0.8026); Very rare (popmax 0.00593%, nfe).

How common is BAIAP2 p.Met79Val (c.235A>G) in the general population?

BAIAP2 p.Met79Val (c.235A>G) is very rare (popmax 0.00593%, nfe) (gnomAD).

What do computational predictors say about BAIAP2 p.Met79Val (c.235A>G)?

AlphaMissense predicts likely pathogenic (score 0.8026) — an in-silico prediction, not a clinical call.

BAIAP2 p.Met79Val

c.235A>G · VCV3260297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8026 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00593%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8026	likely pathogenic
REVEL	0.184	benign-leaning
SaProt	LLR -11.21	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 69 kb · p 0.0018 · regional, not allelic
Overall
CADD	29.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00593% European (non-Finnish) · 70/1,180,012 alleles

Filtering AF 0.00478% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00439%

Overall 0.00446% 72/1,613,790 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00593%	16,857
East Asian	0.00223%	44,866
South Asian	0.0011%	91,084

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: BAIAP2
Protein: p.Met79Val
Coding: c.235A>G
MANE Select: NM_001144888
Type: single nucleotide variant
Location: chr17:81084849 (GRCh38)
Gene constraint: LOEUF 0.446 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.81 · 12 PDB
Residue 79: the imd domain; an α-helix

Full BAIAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAIAP2 c.1269-7C>T Likely benign ★★ same type
BAIAP2 c.643-9C>T Benign ★★ same type
BAIAP2 p.Gln449= Benign ★★ same type
BAIAP2 p.Pro522= Benign/Likely benign ★★ same type
BAIAP2 p.Thr185= Benign ★★ same type
BAIAP2 p.Val204= Benign ★★ same type
BAIAP2 c.1535+1763T>G Uncertain significance ★ same type
BAIAP2 c.1535+553G>A 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/baiap2-p-met79val (accessed [today's date]).

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