BCAP31

B cell receptor associated protein 31

Basic information

Region (hg38): X:153700491-153724565

Links

ENSG00000185825 ∙ NCBI:10134 ∙ OMIM:300398 ∙ HGNC:16695 ∙ Uniprot:P51572 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (Strong), mode of inheritance: XL
• severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (Strong), mode of inheritance: XL
• severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (Supportive), mode of inheritance: AR
• severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, dystonia, and cerebral hypomyelination	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Neurologic	24011989

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCAP31 gene.

• not provided (122 variants)
• Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (9 variants)
• Inborn genetic diseases (9 variants)
• not specified (1 variants)
• Seizure;Global developmental delay (1 variants)
• BCAP31-Related Disorder (1 variants)
• BCAP31-related condition (1 variants)
• Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAP31 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	22	1	25
missense			36	3	1	40
nonsense	2					2
start loss						0
frameshift	3		2			5
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			2	3	1	6
non coding			1	23	19	43
Total	6	1	42	48	21

Variants in BCAP31

This is a list of pathogenic ClinVar variants found in the BCAP31 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-153700939-A-G		Inborn genetic diseases	Likely pathogenic (Nov 09, 2017)
X-153700941-TCTTC-T			Uncertain significance (Oct 01, 2018)
X-153700945-C-T		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
X-153700956-A-G			Uncertain significance (May 10, 2022)
X-153700957-T-TG			Uncertain significance (Jun 08, 2022)
X-153700959-G-A			Uncertain significance (Nov 27, 2023)
X-153700959-G-C			Uncertain significance (Jan 06, 2024)
X-153700962-C-T		Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome	Uncertain significance (Oct 04, 2023)
X-153700964-A-G			Likely benign (Mar 01, 2022)
X-153700965-T-A		Microcephaly • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jun 23, 2023)
X-153700969-C-G		Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome	Uncertain significance (Jul 28, 2020)
X-153700972-C-T			Benign (Nov 28, 2023)
X-153700974-G-A			Uncertain significance (Aug 04, 2023)
X-153700975-C-T		BCAP31-related disorder	Uncertain significance (Dec 22, 2023)
X-153701109-GC-G			Benign (Jul 05, 2018)
X-153701993-A-G			Likely benign (Jan 01, 2023)
X-153701994-C-T			Benign (Aug 17, 2023)
X-153701995-G-A			Likely benign (Jul 21, 2023)
X-153701999-G-A			Likely benign (Nov 16, 2022)
X-153702019-G-A			Likely benign (Aug 17, 2023)
X-153702033-A-C			Uncertain significance (Oct 01, 2023)
X-153702040-G-A			Likely benign (Jan 09, 2024)
X-153702047-T-A			Uncertain significance (Aug 28, 2022)
X-153702072-G-A			Uncertain significance (Feb 10, 2023)
X-153702090-T-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Feb 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAP31	protein_coding	protein_coding	ENST00000458587	8	24206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.434	0.560	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	82	123	0.669	0.00000977	2024
Missense in Polyphen		22	49.524	0.44423		768
Synonymous	0.136	53	54.3	0.976	0.00000454	626
Loss of Function	2.29	2	9.69	0.206	6.11e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a chaperone protein. Is one of the most abundant endoplasmic reticulum (ER) proteins. Plays a role in the export of secreted proteins in the ER, the recognition of abnormally folded protein and their targeting to the ER associated-degradation (ERAD). Also serves as a cargo receptor for the export of transmembrane proteins. May be involved in CASP8- mediated apoptosis. {ECO:0000269|PubMed:10958671, ECO:0000269|PubMed:18287538, ECO:0000269|PubMed:9396746}.
• Disease: DISEASE: Deafness, dystonia, and cerebral hypomyelination (DDCH) [MIM:300475]: An X-linked recessive mental retardation syndrome characterized by almost no psychomotor development, dysmorphic facial features, sensorineural deafness, dystonia, pyramidal signs, and hypomyelination on brain imaging. {ECO:0000269|PubMed:24011989}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=BCAP31 is deleted in the chromosome Xq28 deletion syndrome which involves BCAP31 and the and the promoter region of ABCD1. {ECO:0000269|PubMed:11992258}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.208
• hipred: Y
• hipred_score: 0.598
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bcap31

Gene ontology

• Biological process: antigen processing and presentation of peptide antigen via MHC class I;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;apoptotic process;positive regulation of cytosolic calcium ion concentration;spermatogenesis;negative regulation of endoplasmic reticulum calcium ion concentration;calcium-mediated signaling using intracellular calcium source;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of mitochondrial calcium ion concentration;protein localization to endoplasmic reticulum exit site;positive regulation of ER-associated ubiquitin-dependent protein catabolic process;positive regulation of retrograde protein transport, ER to cytosol;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: mitochondrion;endoplasmic reticulum;Sec61 translocon complex;endoplasmic reticulum membrane;lipid droplet;cytosol;integral component of plasma membrane;membrane;clathrin-coated vesicle;Golgi cisterna membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;integral component of lumenal side of endoplasmic reticulum membrane;perinuclear endoplasmic reticulum
• Molecular function: protein binding;MHC class I protein binding;protein-containing complex binding