RBPMS2

RNA binding protein, mRNA processing factor 2, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:64739891-64775589

Links

ENSG00000166831 ∙ NCBI:348093 ∙ OMIM:619034 ∙ HGNC:19098 ∙ Uniprot:Q6ZRY4 ∙ 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 RBPMS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBPMS2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in RBPMS2

This is a list of pathogenic ClinVar variants found in the RBPMS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64741194-G-T		not specified	Uncertain significance (Mar 23, 2022)
15-64741214-G-A		not specified	Uncertain significance (Mar 01, 2024)
15-64748424-C-T		not specified	Uncertain significance (Nov 06, 2023)
15-64748442-C-T		not specified	Uncertain significance (Oct 26, 2021)
15-64748483-G-A		not specified	Uncertain significance (Sep 13, 2023)
15-64748502-T-C		not specified	Uncertain significance (Apr 20, 2024)
15-64748517-G-T		not specified	Uncertain significance (Aug 21, 2023)
15-64748547-G-C		not specified	Uncertain significance (Apr 20, 2023)
15-64748553-C-A		not specified	Uncertain significance (Mar 07, 2024)
15-64748555-C-T		not specified	Uncertain significance (Sep 26, 2024)
15-64749012-C-T		not specified	Uncertain significance (Dec 12, 2023)
15-64749014-A-G		not specified	Uncertain significance (Sep 25, 2023)
15-64749042-C-T		not specified	Uncertain significance (Aug 03, 2022)
15-64749059-G-A		not specified	Uncertain significance (Feb 21, 2024)
15-64749069-G-T		not specified	Uncertain significance (Jan 25, 2024)
15-64749143-C-T		not specified	Uncertain significance (Mar 12, 2024)
15-64750351-C-T		not specified	Uncertain significance (Sep 20, 2024)
15-64751572-G-A		not specified	Uncertain significance (Dec 15, 2022)
15-64751635-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-64775312-T-C		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBPMS2	protein_coding	protein_coding	ENST00000300069	7	35696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.877	0.123	125737	0	2	125739	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.937	91	120	0.759	0.00000720	1325
Missense in Polyphen		21	38.799	0.54125		425
Synonymous	-0.706	56	49.7	1.13	0.00000332	433
Loss of Function	2.83	1	11.2	0.0892	5.75e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the regulation of smooth muscle cell differentiation and proliferation in the gastrointestinal system. Binds NOG mRNA. Mediates an increase of NOG mRNA levels, and thereby contributes to the negative regulation of the BMP signaling pathway. This promotes reversible dedifferentiation of smooth muscle cells and promotes smooth muscle cell proliferation. {ECO:0000250|UniProtKB:Q9W6I1}.

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.251
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.770
• hipred: N
• hipred_score: 0.441
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbpms2

Gene ontology

• Biological process: mRNA splicing, via spliceosome;negative regulation of BMP signaling pathway;embryonic digestive tract morphogenesis;positive regulation of smooth muscle cell proliferation;negative regulation of smooth muscle cell differentiation
• Cellular component: cytoplasm
• Molecular function: mRNA binding;protein binding;snRNA stem-loop binding;protein homodimerization activity