Is BCAP31 p.Ala106Val (c.317C>T) pathogenic?

BCAP31 p.Ala106Val (c.317C>T) is classified Uncertain significance in BCAP31 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-26). AlphaMissense: likely pathogenic (0.8376); Absent from gnomAD v4.1; Associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome.

How common is BCAP31 p.Ala106Val (c.317C>T) in the general population?

BCAP31 p.Ala106Val (c.317C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCAP31 p.Ala106Val (c.317C>T)?

AlphaMissense predicts likely pathogenic (score 0.8376) — an in-silico prediction, not a clinical call.

BCAP31 p.Ala106Val

Q: What condition is associated with BCAP31 p.Ala106Val (c.317C>T)?

BCAP31 p.Ala106Val (c.317C>T) is associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (ClinVar).

c.317C>T · rs2091621117 · VCV976022

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8376 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome

Computational evidence

Protein change
AlphaMissense	0.8376	likely pathogenic
REVEL	0.325	indeterminate
SaProt	LLR -9.49	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 0.64	unconstrained · MANE · 22 kb · p 6.9e-07 · regional, not allelic
Overall
CADD	27.7	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

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: BCAP31
Protein: p.Ala106Val
Coding: c.317C>T
MANE Select: NM_001256447
dbSNP: rs2091621117
Type: single nucleotide variant
Location: chrX:153715566 (GRCh38)
Structure: AlphaFold pLDDT 84.74 · 3 PDB

Full BCAP31 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCAP31 p.Gly239Asp Uncertain significance ★★ ⚠ same condition
BCAP31 c.341+2T>G Pathogenic ★ same condition
BCAP31 p.Gln139Ter Pathogenic ★ same condition
BCAP31 p.Gln156Ter Likely pathogenic ★ same condition
BCAP31 p.Arg31Lys Uncertain significance ★ ⚠ same condition
BCAP31 p.Asp164Glu Uncertain significance ★ ⚠ same condition
BCAP31 p.Val237Leu Uncertain significance ★ ⚠ same condition
BCAP31 c.194-2A>G Pathogenic same condition

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/bcap31-p-ala106val (accessed [today's date]).

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