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.

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.

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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SNAPC1

This is a list of pathogenic ClinVar variants found in the SNAPC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-61762470-C-T		not specified	Uncertain significance (Oct 01, 2024)
14-61762498-C-T		not specified	Uncertain significance (Dec 10, 2024)
14-61762581-A-G		not specified	Uncertain significance (Jul 30, 2024)
14-61766904-A-C		not specified	Uncertain significance (Aug 14, 2024)
14-61766908-T-C		not specified	Uncertain significance (Aug 13, 2021)
14-61766917-A-T		not specified	Uncertain significance (Dec 02, 2022)
14-61766936-G-C		not specified	Uncertain significance (May 11, 2022)
14-61766950-C-G		not specified	Uncertain significance (Jun 08, 2022)
14-61766995-A-G		not specified	Uncertain significance (Sep 26, 2023)
14-61767015-C-A		not specified	Uncertain significance (May 28, 2024)
14-61767312-G-A		not specified	Uncertain significance (Nov 30, 2022)
14-61768648-A-T		not specified	Uncertain significance (Sep 15, 2021)
14-61768699-A-G		not specified	Uncertain significance (Mar 07, 2024)
14-61768702-G-A		not specified	Uncertain significance (Aug 17, 2021)
14-61768705-C-T		not specified	Uncertain significance (Nov 08, 2022)
14-61776120-A-G		not specified	Uncertain significance (Jul 11, 2023)
14-61776207-T-C		not specified	Uncertain significance (Aug 17, 2021)
14-61778887-A-G		not specified	Uncertain significance (Nov 23, 2022)
14-61782269-G-C		not specified	Uncertain significance (Sep 03, 2024)
14-61782293-A-G		not specified	Uncertain significance (Dec 15, 2022)
14-61782321-A-C		not specified	Uncertain significance (Apr 09, 2024)
14-61782347-A-G		not specified	Uncertain significance (Dec 26, 2023)
14-61782352-G-A		not specified	Uncertain significance (Apr 16, 2024)
14-61782356-G-A		not specified	Uncertain significance (Dec 14, 2023)
14-61782365-C-T		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAPC1	protein_coding	protein_coding	ENST00000216294	10	34072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-16	0.00432	124906	2	839	125747	0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.000465	180	180	1.00	0.00000838	2435
Missense in Polyphen		35	41.218	0.84914		583
Synonymous	-0.650	69	62.5	1.10	0.00000287	625
Loss of Function	-0.338	23	21.3	1.08	0.00000116	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00326	0.00324
Ashkenazi Jewish	0.000109	0.0000992
East Asian	0.000219	0.000217
Finnish	0.00348	0.00347
European (Non-Finnish)	0.00546	0.00539
Middle Eastern	0.000219	0.000217
South Asian	0.00145	0.00141
Other	0.00473	0.00457

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

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

Mouse Genome Informatics

• Gene name: Snapc1

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