GeneBe

SNAPC5

small nuclear RNA activating complex polypeptide 5, the group of SNAP complex |MicroRNA protein coding host genes

Basic information

Region (hg38): 15:66490135-66497780

Links

ENSG00000174446 ∙ NCBI:10302 ∙ OMIM:605979 ∙ HGNC:15484 ∙ Uniprot:O75971 ∙ 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 SNAPC5 gene.

  • not_specified (16 variants)
  • Long_QT_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAPC5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001329615.2. 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
16
clinvar
1
clinvar
 17
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 16 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNAPC5protein_codingprotein_codingENST00000316634 37679
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0002010.3001257260201257460.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7246651.41.280.00000230636
Missense in Polyphen2014.7291.3579189
Synonymous-1.122922.31.300.00000106189
Loss of Function-0.43354.061.231.70e-753

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003220.000322
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.0003260.000326
South Asian0.00003270.0000327
Other0.000.00

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.;
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
0.113

Intolerance Scores

loftool
0.511
rvis_EVS
-0.1
rvis_percentile_EVS
46.2

Haploinsufficiency Scores

pHI
0.0822
hipred
N
hipred_score
0.338
ghis
0.639

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.977

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snapc5
Phenotype

Gene ontology

Biological process
regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription initiation from RNA polymerase III promoter;snRNA transcription by RNA polymerase II
Cellular component
nucleus;nucleoplasm;nucleolus;nuclear body
Molecular function
DNA-binding transcription factor activity;protein binding