RBMS1

RNA binding motif single stranded interacting protein 1, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:160272150-160493807

Previous symbols: [ "C2orf12" ]

Links

ENSG00000153250 ∙ NCBI:5937 ∙ OMIM:602310 ∙ HGNC:9907 ∙ Uniprot:P29558 ∙ 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 RBMS1 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMS1 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			10			10
nonsense						0
start loss			2			2
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	12	0	0

Variants in RBMS1

This is a list of pathogenic ClinVar variants found in the RBMS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-160275674-T-C		not specified	Uncertain significance (May 09, 2023)
2-160277353-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-160277370-G-A		not specified	Uncertain significance (Jun 30, 2023)
2-160278553-C-T		not specified	Uncertain significance (Mar 20, 2023)
2-160278604-T-C		not specified	Uncertain significance (Nov 01, 2022)
2-160278637-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-160281360-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-160284798-C-A		not specified	Uncertain significance (Nov 07, 2022)
2-160287039-T-G		not specified	Uncertain significance (Oct 10, 2023)
2-160287084-G-T		not specified	Uncertain significance (Jun 27, 2023)
2-160300713-T-C		not specified	Uncertain significance (Aug 23, 2021)
2-160303325-C-T			Likely benign (Aug 01, 2022)
2-160303357-C-T		not specified	Uncertain significance (Jul 19, 2023)
2-160318179-G-T		not specified	Uncertain significance (Sep 20, 2023)
2-160367366-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-160367366-A-T		not specified	Uncertain significance (Mar 31, 2022)
2-160367373-G-A		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMS1	protein_coding	protein_coding	ENST00000348849	13	221644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.119	0.881	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	156	226	0.689	0.0000114	2659
Missense in Polyphen		29	74.11	0.39131		866
Synonymous	-1.90	100	78.6	1.27	0.00000427	758
Loss of Function	3.57	7	27.1	0.259	0.00000134	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded DNA binding protein that interacts with the region upstream of the MYC gene. Binds specifically to the DNA sequence motif 5'-[AT]CT[AT][AT]T-3'. Probably has a role in DNA replication.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.365
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.934
• hipred: Y
• hipred_score: 0.654
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.618

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbms1
• 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); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: DNA replication;RNA processing
• Cellular component: nucleus;cytoplasm;cytosol;ribonucleoprotein complex
• Molecular function: double-stranded DNA binding;single-stranded DNA binding;RNA binding;mRNA 3'-UTR binding;protein binding;poly(A) binding;poly(U) RNA binding