Is BCAP31 c.477+8del pathogenic?

BCAP31 c.477+8del is classified Uncertain significance in BCAP31 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-03). Very rare (popmax 0.00703%, sas); Associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome.

How common is BCAP31 c.477+8del in the general population?

BCAP31 c.477+8del is very rare (popmax 0.00703%, sas) (gnomAD).

BCAP31 c.477+8del

Q: What condition is associated with BCAP31 c.477+8del?

BCAP31 c.477+8del is associated with severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (ClinVar).

rs1557047908 · VCV2439483

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00703%, sas)

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.
Splicing
Splice region	donor +8	near-intronic (+8 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.2	GERP -2.2
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00703% South Asian · 4/56,939 alleles

Filtering AF 0.00234% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0014%

Overall 0.000547% 6/1,096,278 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00703%	14,235
Remaining individualsnot grpmax-eligible	0.00421%	23,780

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: BCAP31
Coding: c.477+8del
MANE Select: NM_001256447
dbSNP: rs1557047908
Type: Deletion
Location: chrX:153703951 (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.Gly165fs Likely pathogenic ★ same condition
BCAP31 p.Leu122fs Pathogenic ★★ same condition
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

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-c-477-plus-8del (accessed [today's date]).

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