Is BCAP31 p.Gln33Ter (c.97C>T) pathogenic?

BCAP31 p.Gln33Ter (c.97C>T) is classified Pathogenic in BCAP31 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2013-09-05). Absent from gnomAD v4.1; Associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome.

How common is BCAP31 p.Gln33Ter (c.97C>T) in the general population?

BCAP31 p.Gln33Ter (c.97C>T) is absent from gnomAD v4.1 (gnomAD).

BCAP31 p.Gln33Ter

Q: What condition is associated with BCAP31 p.Gln33Ter (c.97C>T)?

BCAP31 p.Gln33Ter (c.97C>T) is associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (ClinVar).

c.97C>T · rs397515620 · VCV68446

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 8
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Overall
CADD	37.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Gln33Ter
Coding: c.97C>T
MANE Select: NM_001256447
dbSNP: rs397515620
Type: single nucleotide variant
Location: chrX:153720968 (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.Ala106Val Uncertain significance ★ ⚠ same condition
BCAP31 p.Arg31Lys Uncertain significance ★ ⚠ same condition
BCAP31 p.Asp164Glu Uncertain significance ★ ⚠ same condition
BCAP31 p.Val237Leu Uncertain significance ★ ⚠ 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-gln33ter (accessed [today's date]).

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