SNRNP40

small nuclear ribonucleoprotein U5 subunit 40, the group of Spliceosomal Bact complex|Spliceosomal P complex|WD repeat domain containing|Spliceosomal C complex|U5 small nuclear ribonucleoprotein

Basic information

Region (hg38): 1:31259568-31296788

Previous symbols: [ "WDR57" ]

Links

ENSG00000060688NCBI:9410OMIM:607797HGNC:30857Uniprot:Q96DI7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRNP40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP40 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
22
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 22 0 0

Variants in SNRNP40

This is a list of pathogenic ClinVar variants found in the SNRNP40 region.

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

Position Type Phenotype Significance ClinVar
1-31261561-T-C not specified Uncertain significance (Oct 01, 2024)3446752
1-31261574-C-T not specified Uncertain significance (Sep 08, 2024)3446754
1-31261589-T-C not specified Uncertain significance (Feb 08, 2023)2482356
1-31267877-G-A not specified Uncertain significance (Jan 07, 2025)3799521
1-31267911-A-C not specified Uncertain significance (Jan 30, 2024)3167026
1-31271416-T-G not specified Uncertain significance (Dec 15, 2022)2223546
1-31271453-T-C not specified Uncertain significance (Jul 19, 2023)2613053
1-31281423-T-C not specified Uncertain significance (Apr 05, 2023)2525756
1-31281445-G-T not specified Uncertain significance (Feb 23, 2023)2488485
1-31281450-G-A not specified Uncertain significance (Mar 24, 2023)2519399
1-31281467-G-C not specified Uncertain significance (Nov 10, 2022)2325563
1-31291925-T-C not specified Uncertain significance (May 23, 2023)2549758
1-31291951-A-T not specified Uncertain significance (Jun 07, 2024)3321202
1-31291991-T-C not specified Uncertain significance (Sep 20, 2024)3446753
1-31293225-G-C not specified Uncertain significance (Aug 17, 2022)2307908
1-31293329-G-A not specified Uncertain significance (Oct 12, 2022)2318453
1-31293341-G-A not specified Uncertain significance (Jan 22, 2024)3167023
1-31296612-G-A not specified Uncertain significance (Dec 31, 2023)3167022
1-31296618-A-G not specified Uncertain significance (Dec 31, 2023)3167021
1-31296649-C-G not specified Uncertain significance (Apr 11, 2023)2536035
1-31296669-G-A not specified Uncertain significance (Apr 20, 2023)2539723
1-31296714-G-A not specified Uncertain significance (Mar 01, 2023)2492096
1-31296732-C-A not specified Uncertain significance (Dec 13, 2023)3167024

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNRNP40protein_codingprotein_codingENST00000263694 1037246
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8530.1471257240221257460.0000875
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.551361970.6900.000009682324
Missense in Polyphen3373.0270.45189871
Synonymous0.05897676.70.9910.00000395696
Loss of Function3.46319.50.1549.09e-7237

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008830.0000883
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001680.000167
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs. {ECO:0000269|PubMed:9774689}.;
Pathway
Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
0.320
rvis_EVS
-0.36
rvis_percentile_EVS
28.63

Haploinsufficiency Scores

pHI
0.290
hipred
Y
hipred_score
0.816
ghis
0.692

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.149

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snrnp40
Phenotype

Gene ontology

Biological process
RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA processing;RNA splicing
Cellular component
nucleoplasm;U5 snRNP;small nucleolar ribonucleoprotein complex;cytosol;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
Molecular function
RNA binding;protein binding