BCAP31

Chr XXLR

B cell receptor associated protein 31

Also known as: 6C6-AG, BAP31, CDM, DDCH, DELXQ28, DXS1357E, MICRODELXq28

NCBI Gene: 10134ENSG00000185825UniProt: P51572

This gene encodes a member of the B-cell receptor associated protein 31 superfamily. The encoded protein is a multi-pass transmembrane protein of the endoplasmic reticulum that is involved in the anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi and in caspase 8-mediated apoptosis. Microdeletions in this gene are associated with contiguous ABCD1/DXS1375E deletion syndrome (CADDS), a neonatal disorder. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 16. [provided by RefSeq, Jan 2012]

Primary Disease Associations & Inheritance

Deafness, dystonia, and cerebral hypomyelinationMIM #300475
XLR
516
ClinVar variants
130
Pathogenic / LP
0.43
pLI score
0
Active trials
Clinical Summary— BCAP31
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.21) despite low pLI — interpret in context.
📋
ClinVar Variants
130 Pathogenic / Likely Pathogenic· 104 VUS of 516 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.65LOEUF
pLI 0.434
Z-score 2.29
OE 0.21 (0.08–0.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.30Z-score
OE missense 0.67 (0.56–0.80)
82 obs / 122.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.21 (0.08–0.65)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.67 (0.56–0.80)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.98
0≤1.21.6
LoF obs/exp: 2 / 9.7Missense obs/exp: 82 / 122.5Syn Z: 0.14

ClinVar Variant Classifications

516 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic122
Likely Pathogenic8
VUS104
Likely Benign89
Benign25
Conflicting11
122
Pathogenic
8
Likely Pathogenic
104
VUS
89
Likely Benign
25
Benign
11
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
4
0
118
0
122
Likely Pathogenic
2
1
5
0
8
VUS
2
69
32
1
104
Likely Benign
0
7
43
39
89
Benign
2
1
19
3
25
Conflicting
—11
Total107821743359

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BCAP31 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

BCAP31-related deafness, dystonia, and central hypomyelination with disorganization of the Golgi apparatus

definitive
Monoallelic X HemizygousLoss Of FunctionAbsent Gene Product
Dev. DisordersEar
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Deafness, dystonia, and cerebral hypomyelination

MIM #300475

Molecular basis of disorder known

X-linked recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
A novel BCAP31 variant associated with nonsyndromic auditory neuropathy spectrum disorder: mitochondrial dysfunction, cisplatin sensitivity, and amenability to mitochondrial transplantation.
Kim Y et al.·J Transl Med
2025
Genotype-phenotype correlation of contiguous gene deletions of SLC6A8, BCAP31 and ABCD1.
van de Kamp JM et al.·Clin Genet
2015
BCAP 31 expression and promoter demethylation in psoriasis.
Ruchusatsawat K et al.·Asian Pac J Allergy Immunol
2017
BCAP31 is involved in modulating colorectal cancer cell proliferation via the Emerin/β-catenin axis.
Han L et al.·Exp Cell Res
2022
Utility of genome sequencing in exome-negative pediatric patients with neurodevelopmental phenotypes.
Nomakuchi TT et al.·Am J Med Genet A
2024Cohort
An X-Linked Ataxia Syndrome in a Family with Hearing Loss Associated with a Novel Variant in the BCAP31 Gene.
Paucar M et al.·Mov Disord
2025Case report
BCAP31 drives TNBC development by modulating ligand-independent EGFR trafficking and spontaneous EGFR phosphorylation.
Fu W et al.·Theranostics
2019
Further delineation of BCAP31-linked intellectual disability: description of 17 new families with LoF and missense variants.
Whalen S et al.·Eur J Hum Genet
2021Case report
Mutations in BCAP31 cause a severe X-linked phenotype with deafness, dystonia, and central hypomyelination and disorganize the Golgi apparatus.
Cacciagli P et al.·Am J Hum Genet
2013
BCAP31-related syndrome: The first de novo report.
Rinaldi B et al.·Eur J Med Genet
2020Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools