BRK1

BRICK1 subunit of SCAR/WAVE actin nucleating complex, the group of SCAR/WAVE complex

Basic information

Region (hg38): 3:10115675-10127190

Previous symbols: [ "C3orf10" ]

Links

ENSG00000254999 ∙ NCBI:55845 ∙ OMIM:611183 ∙ HGNC:23057 ∙ Uniprot:Q8WUW1 ∙ 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 BRK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRK1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					79	79
Total	0	0	0	0	79

Variants in BRK1

This is a list of pathogenic ClinVar variants found in the BRK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-10115684-C-T			Benign (Jul 05, 2018)
3-10115914-C-A			Benign (Jul 06, 2018)
3-10116418-GTA-G			Benign (Jul 06, 2018)
3-10116618-C-G			Benign (Jul 06, 2018)
3-10116709-A-G			Benign (Jul 06, 2018)
3-10117393-CT-C			Benign (Aug 19, 2019)
3-10117393-C-CT			Benign (Aug 07, 2019)
3-10118112-G-A			Benign (Jul 14, 2018)
3-10118114-A-G			Benign (Jul 06, 2018)
3-10118252-C-A			Benign (Aug 15, 2019)
3-10118252-C-CAAAAA			Benign (Aug 16, 2019)
3-10118252-C-CAAAAAA			Benign (Aug 16, 2019)
3-10118448-C-T			Benign (Jul 06, 2018)
3-10118575-T-C			Benign (Jul 06, 2018)
3-10119001-T-TTTTG			Benign (Aug 15, 2019)
3-10119143-C-A			Benign (Apr 01, 2020)
3-10119143-C-CA			Benign (Aug 16, 2019)
3-10119143-C-CAA			Benign (Aug 19, 2019)
3-10119207-A-G			Benign (Jul 06, 2018)
3-10119431-C-G			Benign (Jul 14, 2018)
3-10119721-G-T			Benign (Jul 06, 2018)
3-10119834-C-A			Benign (Jul 06, 2018)
3-10120037-G-GT			Benign (Aug 30, 2019)
3-10120199-C-CT			Benign (Aug 19, 2019)
3-10121189-G-T			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRK1	protein_coding	protein_coding	ENST00000530758	3	11599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.687	0.296	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	20	42.0	0.476	0.00000217	481
Missense in Polyphen		1	4.1293	0.24217		57
Synonymous	-0.953	19	14.4	1.32	7.30e-7	137
Loss of Function	1.81	0	3.80	0.00	1.61e-7	48

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: Involved in regulation of actin and microtubule organization. Part of a WAVE complex that activates the Arp2/3 complex. As component of the WAVE1 complex, required for BDNF- NTRK2 endocytic trafficking and signaling from early endosomes (By similarity). {ECO:0000250|UniProtKB:Q91VR8, ECO:0000269|PubMed:18560548}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Regulation of Actin Cytoskeleton;Signal Transduction;VEGFA-VEGFR2 Pathway;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;ErbB1 downstream signaling;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;RAC1 signaling pathway;PDGFR-beta signaling pathway (Consensus)

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.471
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brk1
• Phenotype: growth/size/body region phenotype; cellular phenotype; embryo phenotype; reproductive system 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)

Gene ontology

• Biological process: in utero embryonic development;actin filament organization;regulation of actin polymerization or depolymerization;positive regulation of cell population proliferation;positive regulation of lamellipodium assembly;Rac protein signal transduction;positive regulation of protein complex assembly;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;cell motility;protein homotrimerization;positive regulation of Arp2/3 complex-mediated actin nucleation
• Cellular component: cytosol;cytoskeleton;lamellipodium;SCAR complex;extracellular exosome
• Molecular function: protein binding;identical protein binding;protein-containing complex binding;Rac GTPase binding