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.

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.

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			48	5		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	52	6	0

Variants in SNAPC2

This is a list of pathogenic ClinVar variants found in the SNAPC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-7920373-C-T		not specified	Uncertain significance (Dec 25, 2024)
19-7920377-C-G		not specified	Uncertain significance (May 04, 2023)
19-7920394-G-T		not specified	Uncertain significance (Mar 28, 2024)
19-7920395-C-T		not specified	Uncertain significance (Apr 23, 2024)
19-7920397-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-7920403-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-7920415-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-7920425-G-C		not specified	Uncertain significance (Aug 16, 2022)
19-7920428-C-T		not specified	Uncertain significance (Feb 08, 2025)
19-7920431-C-T		not specified	Uncertain significance (Aug 19, 2024)
19-7920469-C-T		not specified	Uncertain significance (Aug 28, 2024)
19-7920499-C-A		not specified	Uncertain significance (Feb 27, 2023)
19-7920509-C-G		not specified	Uncertain significance (Oct 29, 2024)
19-7920525-G-C		not specified	Uncertain significance (Dec 27, 2022)
19-7920535-C-G		not specified	Uncertain significance (Oct 27, 2022)
19-7920536-G-C		not specified	Uncertain significance (Dec 19, 2022)
19-7920538-A-G		not specified	Uncertain significance (Mar 14, 2023)
19-7921474-C-A		not specified	Uncertain significance (Mar 22, 2023)
19-7921484-A-C		not specified	Uncertain significance (May 21, 2024)
19-7921516-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-7921532-C-T		not specified	Uncertain significance (Oct 29, 2024)
19-7921537-A-G		not specified	Uncertain significance (Feb 10, 2022)
19-7921711-A-G		not specified	Uncertain significance (May 18, 2022)
19-7921763-C-T		not specified	Uncertain significance (Mar 28, 2023)
19-7922076-C-G		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAPC2	protein_coding	protein_coding	ENST00000221573	5	2935

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.869	125703	0	32	125735	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.46	261	203	1.29	0.0000120	2063
Missense in Polyphen		88	70.433	1.2494		785
Synonymous	-1.89	116	92.8	1.25	0.00000606	783
Loss of Function	1.86	3	9.04	0.332	3.85e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000976	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000295	0.000294
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snapc2

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