Is BAIAP3 p.Ala855Pro (c.2563G>C) pathogenic?

BAIAP3 p.Ala855Pro (c.2563G>C) is classified Likely benign in BAIAP3 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.8445); Absent from gnomAD v4.1; Associated with long QT syndrome.

What condition is associated with BAIAP3 p.Ala855Pro (c.2563G>C)?

BAIAP3 p.Ala855Pro (c.2563G>C) is associated with long QT syndrome (ClinVar).

How common is BAIAP3 p.Ala855Pro (c.2563G>C) in the general population?

BAIAP3 p.Ala855Pro (c.2563G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAIAP3 p.Ala855Pro (c.2563G>C)?

AlphaMissense predicts likely pathogenic (score 0.8445) — an in-silico prediction, not a clinical call.

BAIAP3 p.Ala855Pro

c.2563G>C · rs796052185 · VCV207918

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8445 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

long QT syndrome

Computational evidence

Protein change
AlphaMissense	0.8445	likely pathogenic · top 9% in BAIAP3
REVEL	0.703	pathogenic-leaning
SaProt	LLR -14.13	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	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	27.3	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 A890P vs ClinVar A855P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BAIAP3
Protein: p.Ala855Pro
Coding: c.2563G>C
MANE Select: NM_001199097
dbSNP: rs796052185
Type: single nucleotide variant
Location: chr16:1346605 (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

Disease context

long QT syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-ala855pro (accessed [today's date]).

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