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

ENSG00000166831NCBI:348093OMIM:619034HGNC:19098Uniprot:Q6ZRY4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)2361324
15-64741214-G-A not specified Uncertain significance (Mar 01, 2024)3152628
15-64748424-C-T not specified Uncertain significance (Nov 06, 2023)3152627
15-64748442-C-T not specified Uncertain significance (Oct 26, 2021)2228038
15-64748483-G-A not specified Uncertain significance (Sep 13, 2023)2592489
15-64748502-T-C not specified Uncertain significance (Apr 20, 2024)3313384
15-64748517-G-T not specified Uncertain significance (Aug 21, 2023)2620388
15-64748547-G-C not specified Uncertain significance (Apr 20, 2023)2539677
15-64748553-C-A not specified Uncertain significance (Mar 07, 2024)3152625
15-64748555-C-T not specified Uncertain significance (Sep 26, 2024)3431537
15-64749012-C-T not specified Uncertain significance (Dec 12, 2023)3152624
15-64749014-A-G not specified Uncertain significance (Sep 25, 2023)3152623
15-64749042-C-T not specified Uncertain significance (Aug 03, 2022)2305277
15-64749059-G-A not specified Uncertain significance (Feb 21, 2024)3152622
15-64749069-G-T not specified Uncertain significance (Jan 25, 2024)3152621
15-64749143-C-T not specified Uncertain significance (Mar 12, 2024)3152620
15-64750351-C-T not specified Uncertain significance (Sep 20, 2024)3431539
15-64751572-G-A not specified Uncertain significance (Dec 15, 2022)2343395
15-64751635-G-A not specified Uncertain significance (Aug 08, 2023)2588175
15-64775312-T-C not specified Uncertain significance (May 20, 2024)3313385

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RBPMS2protein_codingprotein_codingENST00000300069 735696
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8770.123125737021257390.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.937911200.7590.000007201325
Missense in Polyphen2138.7990.54125425
Synonymous-0.7065649.71.130.00000332433
Loss of Function2.83111.20.08925.75e-7128

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rbpms2
Phenotype

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