TSNARE1

t-SNARE domain containing 1

Basic information

Region (hg38): 8:142212079-142403182

Links

ENSG00000171045 ∙ NCBI:203062 ∙ ∙ HGNC:26437 ∙ Uniprot:Q96NA8 ∙ 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 TSNARE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSNARE1 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				2	1	3
missense			55	3	1	59
nonsense					1	1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	6	3

Variants in TSNARE1

This is a list of pathogenic ClinVar variants found in the TSNARE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-142229492-G-A			Benign (Dec 31, 2019)
8-142229566-T-G		not specified	Uncertain significance (May 31, 2022)
8-142274789-G-A		not specified	Uncertain significance (Mar 20, 2024)
8-142274792-T-G		not specified	Uncertain significance (May 10, 2024)
8-142274812-C-T		not specified	Uncertain significance (Mar 04, 2024)
8-142274813-G-A		not specified	Uncertain significance (Mar 14, 2023)
8-142274842-T-C		not specified	Uncertain significance (May 10, 2022)
8-142284452-C-T		not specified	Uncertain significance (Dec 17, 2023)
8-142284456-G-C		not specified	Uncertain significance (Aug 17, 2022)
8-142284477-C-T			Likely benign (May 10, 2018)
8-142300512-G-A		not specified	Uncertain significance (Mar 17, 2023)
8-142300518-G-A		not specified	Uncertain significance (Jul 14, 2021)
8-142300550-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-142300631-G-A		not specified	Uncertain significance (Feb 27, 2023)
8-142314403-G-A		not specified	Uncertain significance (Feb 16, 2023)
8-142314404-C-G		not specified	Uncertain significance (Feb 05, 2024)
8-142315011-C-T		not specified	Uncertain significance (Aug 03, 2022)
8-142315014-C-T		not specified	Uncertain significance (Apr 04, 2024)
8-142315022-C-G		not specified	Uncertain significance (Feb 23, 2023)
8-142315028-A-C		not specified	Uncertain significance (Dec 01, 2022)
8-142315059-C-G		not specified	Uncertain significance (Feb 12, 2024)
8-142315068-G-A		not specified	Uncertain significance (Sep 29, 2023)
8-142315071-G-A		not specified	Uncertain significance (Jan 30, 2024)
8-142315085-C-A		not specified	Uncertain significance (Mar 31, 2023)
8-142315086-G-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSNARE1	protein_coding	protein_coding	ENST00000307180	12	191161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.63e-7	0.985	125158	3	585	125746	0.00234

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0540	326	323	1.01	0.0000219	3225
Missense in Polyphen		61	74.123	0.82296		761
Synonymous	0.250	137	141	0.973	0.00000984	1055
Loss of Function	2.22	14	26.3	0.533	0.00000138	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0283	0.0281
Ashkenazi Jewish	0.00421	0.00418
East Asian	0.000110	0.000109
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000518	0.000501
Middle Eastern	0.000110	0.000109
South Asian	0.000101	0.0000980
Other	0.000534	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.914
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.37

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.123
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;vesicle docking
• Cellular component: endomembrane system;integral component of membrane;SNARE complex
• Molecular function: SNARE binding;SNAP receptor activity