SNAPC3

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

Basic information

Region (hg38): 9:15422733-15465953

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.

• Inborn genetic diseases (25 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.

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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	23	2	0

Variants in SNAPC3

This is a list of pathogenic ClinVar variants found in the SNAPC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-15422905-C-G		not specified	Uncertain significance (May 24, 2023)
9-15422908-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-15422913-A-G		not specified	Likely benign (Jul 15, 2021)
9-15422925-G-A		not specified	Uncertain significance (Jul 05, 2023)
9-15422946-G-A		not specified	Likely benign (Feb 27, 2023)
9-15423064-C-T		not specified	Uncertain significance (Jun 22, 2023)
9-15423079-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-15423096-G-C		not specified	Uncertain significance (Oct 18, 2021)
9-15423105-G-T		not specified	Uncertain significance (Jun 29, 2023)
9-15423175-A-C		not specified	Uncertain significance (Apr 07, 2023)
9-15433593-C-T		not specified	Uncertain significance (Aug 09, 2021)
9-15444617-G-A		not specified	Uncertain significance (Jul 12, 2022)
9-15447122-A-G		not specified	Uncertain significance (Mar 23, 2022)
9-15447239-A-G		not specified	Uncertain significance (Jan 31, 2023)
9-15451327-A-T		not specified	Uncertain significance (Dec 13, 2022)
9-15451378-A-C		not specified	Uncertain significance (Jun 02, 2023)
9-15453097-C-A		not specified	Uncertain significance (May 13, 2022)
9-15453186-A-G		not specified	Likely benign (Feb 22, 2024)
9-15457960-G-C		not specified	Uncertain significance (Oct 25, 2022)
9-15458046-T-C		not specified	Uncertain significance (Jan 26, 2022)
9-15459730-A-G		not specified	Uncertain significance (Sep 14, 2023)
9-15459744-G-C		not specified	Uncertain significance (Oct 05, 2021)
9-15459753-G-A		not specified	Uncertain significance (Jul 05, 2022)
9-15459835-A-T		not specified	Uncertain significance (Sep 16, 2021)
9-15459841-A-G		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAPC3	protein_coding	protein_coding	ENST00000380821	9	43250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-7	0.845	125694	0	53	125747	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.03	244	203	1.20	0.00000939	2675
Missense in Polyphen		71	76.441	0.92882		1008
Synonymous	-1.22	89	75.5	1.18	0.00000356	755
Loss of Function	1.50	13	20.3	0.641	0.00000107	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000934	0.000927
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000217	0.000211
Middle Eastern	0.00	0.00
South Asian	0.000166	0.000163
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. {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

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

Mouse Genome Informatics

• Gene name: Snapc3

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