SNRPD1
Basic information
Region (hg38): 18:21612314-21633524
Previous symbols: [ "SNRPD" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| 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) | ||
| 18-21629068-G-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 18-21629107-G-A | not specified | Uncertain significance (Mar 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNRPD1 | protein_coding | protein_coding | ENST00000300413 | 4 | 18190 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.799 | 0.196 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.29 | 15 | 68.4 | 0.219 | 0.00000378 | 757 |
| Missense in Polyphen | 3 | 21.355 | 0.14048 | 270 | ||
| Synonymous | 1.02 | 17 | 23.3 | 0.730 | 0.00000118 | 242 |
| Loss of Function | 2.13 | 0 | 5.31 | 0.00 | 2.88e-7 | 69 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
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