BCAR3

BCAR3 adaptor protein, NSP family member, the group of SH2 domain containing|NSP adaptor proteins

Basic information

Region (hg38): 1:93561741-93847150

Links

ENSG00000137936 ∙ NCBI:8412 ∙ OMIM:604704 ∙ HGNC:973 ∙ Uniprot:O75815 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCAR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAR3 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					1	1
missense			82	7	2	91
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	82	7	3

Variants in BCAR3

This is a list of pathogenic ClinVar variants found in the BCAR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-93562281-C-T		not specified	Uncertain significance (Jan 22, 2025)
1-93562353-C-G		not specified	Uncertain significance (Feb 02, 2025)
1-93562365-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-93562391-T-G		not specified	Uncertain significance (Feb 13, 2025)
1-93567296-G-A		not specified	Uncertain significance (Nov 28, 2023)
1-93567305-C-T			Uncertain significance (Nov 18, 2019)
1-93567341-G-A		not specified	Uncertain significance (May 05, 2022)
1-93567378-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-93567380-T-C			Benign (Apr 16, 2018)
1-93567396-C-T		not specified	Uncertain significance (Jun 16, 2024)
1-93567422-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-93567434-G-A		not specified	Uncertain significance (Dec 02, 2022)
1-93567443-G-A		not specified	Uncertain significance (Nov 10, 2024)
1-93567742-C-G		not specified	Uncertain significance (Dec 07, 2023)
1-93567780-T-G		not specified	Uncertain significance (Mar 20, 2023)
1-93567836-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-93571696-G-A		not specified	Uncertain significance (Nov 08, 2021)
1-93571710-T-C			Benign (Apr 16, 2018)
1-93571727-A-T		not specified	Uncertain significance (Nov 10, 2024)
1-93571773-G-A			Likely benign (Apr 05, 2018)
1-93571810-C-G		not specified	Uncertain significance (Apr 07, 2022)
1-93571837-T-G		not specified	Uncertain significance (Aug 12, 2021)
1-93576020-A-G		not specified	Uncertain significance (Mar 07, 2025)
1-93576033-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-93576045-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAR3	protein_coding	protein_coding	ENST00000370244	11	285360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.582	0.418	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.302	479	498	0.962	0.0000299	5398
Missense in Polyphen		162	173.21	0.93529		1895
Synonymous	0.918	187	204	0.918	0.0000132	1651
Loss of Function	4.48	8	37.7	0.212	0.00000221	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00145
Ashkenazi Jewish	0.000501	0.000496
East Asian	0.000109	0.000109
Finnish	0.0000963	0.0000924
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as an adapter protein and couple activated growth factor receptors to a signaling pathway that regulates the proliferation in breast cancer cells. When overexpressed, it confers anti-estrogen resistance in breast cancer cell lines. May also be regulated by cellular adhesion to extracellular matrix proteins. {ECO:0000269|PubMed:9582273}.
• Pathway: EGFR1;Regulation of CDC42 activity (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.683
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.72

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.749
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcar3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: lens morphogenesis in camera-type eye;signal transduction;small GTPase mediated signal transduction;positive regulation of peptidyl-serine phosphorylation;response to drug
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding