SNRPD1

small nuclear ribonucleoprotein D1 polypeptide, the group of Sm spliceosomal proteins

Basic information

Region (hg38): 18:21612314-21633524

Previous symbols: [ "SNRPD" ]

Links

ENSG00000167088NCBI:6632OMIM:601063HGNC:11158Uniprot:P62314AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPD1 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
3
clinvar
3
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 3 0 0

Variants in SNRPD1

This is a list of pathogenic ClinVar variants found in the SNRPD1 region.

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

Position Type Phenotype Significance ClinVar
18-21623886-A-G not specified Uncertain significance (Oct 09, 2024)3446779
18-21629068-G-C not specified Uncertain significance (Dec 09, 2023)3167055
18-21629107-G-A not specified Uncertain significance (Mar 22, 2023)2527972

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNRPD1protein_codingprotein_codingENST00000300413 418190
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7990.19600000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.291568.40.2190.00000378757
Missense in Polyphen321.3550.14048270
Synonymous1.021723.30.7300.00000118242
Loss of Function2.1305.310.002.88e-769

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP- snRNP interactions through nonspecific electrostatic contacts with RNA. {ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23333303}.;
Pathway
Systemic lupus erythematosus - Homo sapiens (human);Spliceosome - Homo sapiens (human);mRNA Processing;snRNP Assembly;Metabolism of RNA;mRNA Splicing - Major Pathway;Metabolism of non-coding RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.240

Intolerance Scores

loftool
rvis_EVS
0.12
rvis_percentile_EVS
62.38

Haploinsufficiency Scores

pHI
0.864
hipred
Y
hipred_score
0.748
ghis
0.668

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.970

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Snrpd1
Phenotype

Zebrafish Information Network

Gene name
snrpd1
Affected structure
trunk
Phenotype tag
abnormal
Phenotype quality
necrotic

Gene ontology

Biological process
spliceosomal complex assembly;spliceosomal snRNP assembly;mRNA splicing, via spliceosome;RNA splicing;import into nucleus
Cellular component
commitment complex;nucleus;nucleoplasm;U5 snRNP;U1 snRNP;U2 snRNP;U4 snRNP;U12-type spliceosomal complex;cytosol;small nuclear ribonucleoprotein complex;methylosome;pICln-Sm protein complex;SMN-Sm protein complex;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
Molecular function
RNA binding;protein binding;U1 snRNP binding