BRMS1

BRMS1 transcriptional repressor and anoikis regulator

Basic information

Region (hg38): 11:66337333-66345125

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.

not_specified (33 variants)
not_provided (1 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. These statistics are base on transcript: NM_000015399.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	1

Loading clinvar variants...

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