Is BAIAP2 p.Gly485Ser (c.1453G>A) pathogenic?

BAIAP2 p.Gly485Ser (c.1453G>A) is classified Uncertain significance in BAIAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-21). AlphaMissense: likely benign (0.0613); Ultra-rare (popmax 0.03%, sas).

How common is BAIAP2 p.Gly485Ser (c.1453G>A) in the general population?

BAIAP2 p.Gly485Ser (c.1453G>A) is ultra-rare (popmax 0.03%, sas) (gnomAD).

What do computational predictors say about BAIAP2 p.Gly485Ser (c.1453G>A)?

AlphaMissense predicts likely benign (score 0.0613) — an in-silico prediction, not a clinical call.

BAIAP2 p.Gly485Ser

c.1453G>A · VCV3817476

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0613 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.03%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0613	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -5.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.06	GERP -1.5
Regional constraint	o/e 1.16	unconstrained · MANE · 9,028 bp · p 0.11 · regional, not allelic
Overall
CADD	11.49	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.03% South Asian · 27/89,936 alleles

Filtering AF 0.0211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.00486% 78/1,606,254 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.03%	3,331
Remaining individualsnot grpmax-eligible	0.00804%	12,435
East Asian	0.00446%	22,410
European (non-Finnish)	0.0034%	29,417
Admixed American	0.00336%	29,754
African / African-American	0.00267%	37,497

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.Gly485Ser
Coding: c.1453G>A
MANE Select: NM_001144888
Type: single nucleotide variant
Location: chr17:81106860 (GRCh38)
Gene constraint: LOEUF 0.446 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.81 · 12 PDB

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-gly485ser (accessed [today's date]).

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