GeneBe

SNAPC3

small nuclear RNA activating complex polypeptide 3, the group of SNAP complex

Basic information

Region (hg38): 9:15422734-15465953

Links

ENSG00000164975 ∙ NCBI:6619 ∙ OMIM:602348 ∙ HGNC:11136 ∙ Uniprot:Q92966 ∙ 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 SNAPC3 gene.

  • not_specified (62 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAPC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039697.2. 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
59
clinvar
3
clinvar
 62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 59 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNAPC3protein_codingprotein_codingENST00000380821 943250
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.55e-70.8451256940531257470.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.032442031.200.000009392675
Missense in Polyphen7176.4410.928821008
Synonymous-1.228975.51.180.00000356755
Loss of Function1.501320.30.6410.00000107255

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009340.000927
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0002170.000211
Middle Eastern0.000.00
South Asian0.0001660.000163
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. {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
0.108

Intolerance Scores

loftool
0.878
rvis_EVS
-0.07
rvis_percentile_EVS
48.54

Haploinsufficiency Scores

pHI
0.176
hipred
N
hipred_score
0.292
ghis
0.583

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.911

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snapc3
Phenotype

Zebrafish Information Network

Gene name
snapc3
Affected structure
T cell differentiation
Phenotype tag
abnormal
Phenotype quality
decreased occurrence

Gene ontology

Biological process
transcription by RNA polymerase II;transcription by RNA polymerase III;snRNA transcription;snRNA transcription by RNA polymerase II
Cellular component
nucleus;nucleoplasm;nucleolus;nuclear body
Molecular function
DNA binding;protein binding