BCAR1

BCAR1 scaffold protein, Cas family member, the group of Cas scaffold proteins

Basic information

Region (hg38): 16:75228181-75268053

Links

ENSG00000050820 ∙ NCBI:9564 ∙ OMIM:602941 ∙ HGNC:971 ∙ Uniprot:P56945 ∙ 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 BCAR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAR1 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				4	5	9
missense			86	5	8	99
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding					1	1
Total	0	1	86	9	14

Variants in BCAR1

This is a list of pathogenic ClinVar variants found in the BCAR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75229516-C-T		not specified	Uncertain significance (Nov 20, 2024)
16-75229593-T-C		not specified	Uncertain significance (Dec 21, 2022)
16-75229639-T-C		not specified	Uncertain significance (Dec 19, 2022)
16-75229642-C-A		not specified	Uncertain significance (May 26, 2024)
16-75229653-C-T		not specified	Uncertain significance (Nov 29, 2023)
16-75229695-C-T		not specified	Uncertain significance (Dec 26, 2023)
16-75229729-G-C		not specified	Uncertain significance (Apr 23, 2024)
16-75229819-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-75229820-G-A			Likely benign (Apr 23, 2018)
16-75229822-C-T		not specified	Uncertain significance (Oct 25, 2023)
16-75229863-T-C		not specified	Uncertain significance (Feb 13, 2024)
16-75229866-G-A		not specified	Uncertain significance (Oct 20, 2024)
16-75229908-G-A		not specified	Uncertain significance (Apr 13, 2022)
16-75229911-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-75229956-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-75229987-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-75230007-C-T		not specified	Uncertain significance (Feb 13, 2023)
16-75230019-T-C		not specified	Uncertain significance (Jun 16, 2022)
16-75233836-G-A			Benign (Apr 23, 2018)
16-75233851-G-C		not specified	Uncertain significance (Nov 24, 2024)
16-75233868-T-C			Benign (May 14, 2018)
16-75233877-C-T		not specified	Uncertain significance (Aug 09, 2021)
16-75233901-A-G		not specified	Uncertain significance (Aug 20, 2024)
16-75234923-C-G		not specified	Uncertain significance (Sep 26, 2024)
16-75234928-C-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAR1	protein_coding	protein_coding	ENST00000418647	7	39024

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00192	125526	0	2	125528	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.594	609	569	1.07	0.0000383	5733
Missense in Polyphen		303	301.62	1.0046		2968
Synonymous	-2.39	320	270	1.18	0.0000202	2005
Loss of Function	4.71	3	31.5	0.0952	0.00000178	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000649	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000979	0.00000882
Middle Eastern	0.0000649	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Docking protein which plays a central coordinating role for tyrosine kinase-based signaling related to cell adhesion. Implicated in induction of cell migration. Overexpression confers antiestrogen resistance on breast cancer cells. {ECO:0000269|PubMed:12832404, ECO:0000269|PubMed:17038317}.
• Pathway: Focal adhesion - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Integrin-mediated Cell Adhesion;Focal Adhesion;TGF-beta Signaling Pathway;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;miR-509-3p alteration of YAP1-ECM axis;EGF-EGFR Signaling Pathway;Regulation of Actin Cytoskeleton;Signaling by PTK6;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;links between pyk2 and map kinases;angiotensin ii mediated activation of jnk pathway via pyk2 dependent signaling;integrin signaling pathway;pten dependent cell cycle arrest and apoptosis;vegf hypoxia and angiogenesis;VEGFA-VEGFR2 Pathway;Signaling by PDGF;p130Cas linkage to MAPK signaling for integrins;Integrin alphaIIb beta3 signaling;BCR;Platelet Aggregation (Plug Formation);cell to cell adhesion signaling;Platelet activation, signaling and aggregation;Integrin;TGF_beta_Receptor;EGFR1;Integrin signaling;CXCR4-mediated signaling events;Hemostasis;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;Signaling events regulated by Ret tyrosine kinase;Gastrin;Downstream signal transduction;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Osteopontin-mediated events;RAC1 signaling pathway;Alpha9 beta1 integrin signaling events;LPA receptor mediated events;CDC42 signaling events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Netrin-mediated signaling events;Signaling events mediated by focal adhesion kinase;IGF1 pathway;Plasma membrane estrogen receptor signaling;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Alpha4 beta1 integrin signaling events;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B;EPHA2 forward signaling;Endothelins;Integrins in angiogenesis;Signaling events mediated by PRL (Consensus)

Intolerance Scores

• loftool: 0.158
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.51

Haploinsufficiency Scores

• pHI: 0.473
• hipred: Y
• hipred_score: 0.853
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcar1
• Phenotype: growth/size/body region phenotype; cellular phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype

Gene ontology

• Biological process: regulation of cell growth;actin filament organization;cell adhesion;epidermal growth factor receptor signaling pathway;G protein-coupled receptor signaling pathway;integrin-mediated signaling pathway;cell population proliferation;insulin receptor signaling pathway;positive regulation of endothelial cell migration;cell migration;positive regulation of cell migration;cellular response to hepatocyte growth factor stimulus;regulation of apoptotic process;platelet-derived growth factor receptor signaling pathway;vascular endothelial growth factor receptor signaling pathway;neurotrophin TRK receptor signaling pathway;hepatocyte growth factor receptor signaling pathway;antigen receptor-mediated signaling pathway;T cell receptor signaling pathway;B cell receptor signaling pathway;cell division;cell chemotaxis;actin filament reorganization
• Cellular component: ruffle;cytoplasm;cytosol;plasma membrane;focal adhesion;actin cytoskeleton;lamellipodium
• Molecular function: protein binding;SH3 domain binding;protein kinase binding