GeneBe

SNAPC1

small nuclear RNA activating complex polypeptide 1, the group of SNAP complex

Basic information

Region (hg38): 14:61762420-61796428

Links

ENSG00000023608 ∙ NCBI:6617 ∙ OMIM:600591 ∙ HGNC:11134 ∙ Uniprot:Q16533 ∙ 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 SNAPC1 gene.

  • not_specified (38 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAPC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003082.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
38
clinvar
 38
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 38 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNAPC1protein_codingprotein_codingENST00000216294 1034072
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.36e-160.0043212490628391257470.00335
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.0004651801801.000.000008382435
Missense in Polyphen3541.2180.84914583
Synonymous-0.6506962.51.100.00000287625
Loss of Function-0.3382321.31.080.00000116274

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003260.00324
Ashkenazi Jewish0.0001090.0000992
East Asian0.0002190.000217
Finnish0.003480.00347
European (Non-Finnish)0.005460.00539
Middle Eastern0.0002190.000217
South Asian0.001450.00141
Other0.004730.00457

dbNSFP

Source: dbNSFP

Function
FUNCTION: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box. {ECO:0000269|PubMed:12621023}.;
Pathway
Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
0.429
rvis_EVS
0
rvis_percentile_EVS
53.73

Haploinsufficiency Scores

pHI
0.186
hipred
N
hipred_score
0.486
ghis
0.528

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.887

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snapc1
Phenotype

Zebrafish Information Network

Gene name
snapc1b
Affected structure
macrophage
Phenotype tag
abnormal
Phenotype quality
increased size

Gene ontology

Biological process
snRNA transcription by RNA polymerase II;snRNA transcription by RNA polymerase III
Cellular component
nucleus;nucleoplasm;nucleolus;snRNA-activating protein complex
Molecular function
sequence-specific DNA binding