GeneBe

SNAPC2

small nuclear RNA activating complex polypeptide 2, the group of SNAP complex

Basic information

Region (hg38): 19:7920338-7923250

Links

ENSG00000104976 ∙ NCBI:6618 ∙ OMIM:605076 ∙ HGNC:11135 ∙ Uniprot:Q13487 ∙ 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 SNAPC2 gene.

  • not_specified (80 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAPC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003083.4. 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
69
clinvar
11
clinvar
 80
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 69 11 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNAPC2protein_codingprotein_codingENST00000221573 52935
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1010.8691257030321257350.000127
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.462612031.290.00001202063
Missense in Polyphen8870.4331.2494785
Synonymous-1.8911692.81.250.00000606783
Loss of Function1.8639.040.3323.85e-7107

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003580.000358
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00009250.0000924
European (Non-Finnish)0.00009760.0000967
Middle Eastern0.00005440.0000544
South Asian0.0002950.000294
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
0.0972

Intolerance Scores

loftool
0.748
rvis_EVS
0.4
rvis_percentile_EVS
76.31

Haploinsufficiency Scores

pHI
0.0661
hipred
Y
hipred_score
0.508
ghis
0.577

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snapc2
Phenotype

Zebrafish Information Network

Gene name
snapc2
Affected structure
intrahepatic bile duct
Phenotype tag
abnormal
Phenotype quality
degenerate

Gene ontology

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