BRMS1

BRMS1 transcriptional repressor and anoikis regulator

Basic information

Region (hg38): 11:66337332-66345125

Links

ENSG00000174744 ∙ NCBI:25855 ∙ OMIM:606259 ∙ HGNC:17262 ∙ Uniprot:Q9HCU9 ∙ 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 BRMS1 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRMS1 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	1	4
Total	0	0	15	3	2

Variants in BRMS1

This is a list of pathogenic ClinVar variants found in the BRMS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66337677-C-T			Benign (Feb 26, 2018)
11-66337678-G-A		not specified	Likely benign (Feb 28, 2023)
11-66337699-G-A		not specified	Likely benign (Jun 22, 2021)
11-66337732-A-G		not specified	Likely benign (Jan 08, 2024)
11-66337771-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-66337801-C-T		not specified	Likely benign (Aug 12, 2021)
11-66338250-T-A		not specified	Uncertain significance (Dec 17, 2023)
11-66338266-G-A		not specified	Uncertain significance (Aug 08, 2023)
11-66338273-C-T		not specified	Uncertain significance (Feb 11, 2022)
11-66338725-T-C		not specified	Uncertain significance (Jan 18, 2022)
11-66338767-A-G		not specified	Uncertain significance (Jul 13, 2022)
11-66340190-C-T		not specified	Uncertain significance (Dec 20, 2022)
11-66340202-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-66340776-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-66340784-G-A			Benign (Feb 26, 2018)
11-66340797-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-66340837-C-G		not specified	Uncertain significance (Dec 14, 2021)
11-66341032-A-G		not specified	Uncertain significance (May 11, 2022)
11-66341038-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-66341247-C-A		not specified	Uncertain significance (Aug 28, 2023)
11-66341299-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-66341548-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-66341553-C-G		not specified	Uncertain significance (Jun 13, 2022)
11-66341576-C-T		not specified	Uncertain significance (Dec 13, 2021)
11-66341605-T-C		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRMS1	protein_coding	protein_coding	ENST00000425825	9	7793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.58e-7	0.641	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	166	170	0.977	0.0000101	1880
Missense in Polyphen		47	51.471	0.91314		592
Synonymous	0.565	63	69.0	0.913	0.00000406	543
Loss of Function	1.13	13	18.2	0.715	9.59e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000550	0.000544
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000217	0.000217
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Down-regulates transcription activation by NF-kappa-B by promoting the deacetylation of RELA at 'Lys-310'. Promotes HDAC1 binding to promoter regions. Down- regulates expression of anti-apoptotic genes that are controlled by NF-kappa-B. Promotes apoptosis in cells that have inadequate adherence to a substrate, a process called anoikis, and may thereby inhibit metastasis. May be a mediator of metastasis suppression in breast carcinoma. {ECO:0000269|PubMed:14581478, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:20830743}.
• Pathway: HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.157
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.640
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brms1
• Phenotype: homeostasis/metabolism 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: negative regulation of transcription by RNA polymerase II;apoptotic process;histone deacetylation;negative regulation of NF-kappaB transcription factor activity;regulation of apoptotic process;negative regulation of transcription, DNA-templated;positive regulation of protein deacetylation;positive regulation of anoikis
• Cellular component: nucleus;nucleoplasm;cytoplasm;Sin3-type complex
• Molecular function: histone deacetylase activity;protein binding;histone deacetylase binding;NF-kappaB binding