BRAP

BRCA1 associated protein, the group of Ring finger proteins

Basic information

Region (hg38): 12:111642145-111685956

Links

ENSG00000089234 ∙ NCBI:8315 ∙ OMIM:604986 ∙ HGNC:1099 ∙ Uniprot:Q7Z569 ∙ 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 BRAP gene.

• Inborn genetic diseases (17 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRAP 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					5	5
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	17	0	5

Variants in BRAP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-111644212-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-111644218-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-111644221-C-A		not specified	Uncertain significance (Dec 14, 2023)
12-111644248-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-111644252-C-G		not specified	Uncertain significance (Dec 13, 2023)
12-111644281-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-111644438-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-111644444-C-T		not specified	Uncertain significance (Feb 23, 2023)
12-111644536-G-C		not specified	Uncertain significance (Feb 17, 2024)
12-111650001-C-T			Benign (May 08, 2018)
12-111655618-C-T		not specified	Uncertain significance (Nov 18, 2023)
12-111658780-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-111659253-C-T			Benign (Dec 13, 2017)
12-111659295-G-A			Benign (Jun 22, 2018)
12-111660625-T-G		not specified	Uncertain significance (Jun 22, 2021)
12-111660637-A-G		not specified	Uncertain significance (Feb 27, 2023)
12-111660644-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-111665684-T-G		not specified	Uncertain significance (Feb 24, 2022)
12-111665785-G-A			Benign (May 08, 2018)
12-111672686-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-111679205-A-G			Benign (May 08, 2018)
12-111679218-T-C		not specified	Uncertain significance (Mar 24, 2023)
12-111679291-T-C		not specified	Uncertain significance (Jun 22, 2023)
12-111681753-T-G		not specified	Uncertain significance (Nov 10, 2022)
12-111681764-G-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRAP	protein_coding	protein_coding	ENST00000419234	12	43841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000375	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	246	344	0.714	0.0000196	3916
Missense in Polyphen		65	125.42	0.51826		1390
Synonymous	0.134	126	128	0.985	0.00000772	1076
Loss of Function	3.05	15	34.3	0.437	0.00000199	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000217	0.000217
South Asian	0.000133	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates MAP kinase activation by limiting the formation of Raf/MEK complexes probably by inactivation of the KSR1 scaffold protein. Also acts as a Ras responsive E3 ubiquitin ligase that, on activation of Ras, is modified by auto- polyubiquitination resulting in the release of inhibition of Raf/MEK complex formation. May also act as a cytoplasmic retention protein with a role in regulating nuclear transport. {ECO:0000269|PubMed:14724641, ECO:0000303|PubMed:10777491}.
• Pathway: Ras signaling pathway - Homo sapiens (human);Ras Signaling;RAF activation;Disease;Signal Transduction;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.339

Intolerance Scores

• loftool: 0.745
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.540
• hipred: Y
• hipred_score: 0.693
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brap
• Phenotype: embryo 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); 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: MAPK cascade;Ras protein signal transduction;negative regulation of signal transduction;protein ubiquitination
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol;nuclear membrane
• Molecular function: nucleic acid binding;ubiquitin-protein transferase activity;protein binding;nuclear localization sequence binding;zinc ion binding;identical protein binding;ubiquitin protein ligase activity