SNAPC5

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

Basic information

Region (hg38): 15:66490134-66497780

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.

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.

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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SNAPC5

This is a list of pathogenic ClinVar variants found in the SNAPC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-66490357-C-T			Likely benign (Dec 04, 2019)
15-66490358-C-T			Benign (Jan 12, 2020)
15-66490360-C-G			Likely benign (Feb 23, 2021)
15-66490389-C-T			Benign (Dec 07, 2019)
15-66490485-C-T		RASopathy	Likely benign (Nov 04, 2023)
15-66490486-G-A		not specified • RASopathy	Benign (Jan 27, 2024)
15-66490490-C-A		RASopathy	Likely benign (Aug 27, 2023)
15-66490491-C-A		RASopathy	Likely benign (Nov 01, 2022)
15-66490494-A-T		RASopathy	Likely benign (Jul 25, 2023)
15-66490494-AC-A		RASopathy	Likely benign (Nov 25, 2022)
15-66490496-A-G		RASopathy	Likely benign (Jan 22, 2023)
15-66490499-C-T		RASopathy	Uncertain significance (Nov 27, 2023)
15-66490505-C-T		Noonan syndrome • RASopathy	Uncertain significance (Jul 07, 2023)
15-66490514-ATCA-G			Uncertain significance (Nov 09, 2022)
15-66490519-G-A		RASopathy	Likely benign (Nov 17, 2022)
15-66490524-C-A		Cardiovascular phenotype	Uncertain significance (May 17, 2024)
15-66490524-C-T			Uncertain significance (Jul 27, 2022)
15-66490531-T-C		RASopathy • Cardiovascular phenotype	Likely benign (May 09, 2017)
15-66490534-G-A		RASopathy	Likely benign (Mar 26, 2023)
15-66490540-G-A		RASopathy	Likely benign (Nov 24, 2023)
15-66490543-T-C		RASopathy	Likely benign (Jul 19, 2022)
15-66490546-T-G		RASopathy	Uncertain significance (Jul 07, 2023)
15-66490548-C-T		RASopathy	Uncertain significance (Jul 29, 2023)
15-66490549-A-T		RASopathy	Likely benign (Sep 22, 2023)
15-66490552-T-C		Cardiovascular phenotype	Likely benign (Jul 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAPC5	protein_coding	protein_coding	ENST00000316634	3	7679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000201	0.300	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.724	66	51.4	1.28	0.00000230	636
Missense in Polyphen		20	14.729	1.3579		189
Synonymous	-1.12	29	22.3	1.30	0.00000106	189
Loss of Function	-0.433	5	4.06	1.23	1.70e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000326	0.000326
South Asian	0.0000327	0.0000327
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: 0.113

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

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

Mouse Genome Informatics

• Gene name: Snapc5

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