YKT6

YKT6 v-SNARE homolog, the group of SNAREs

Basic information

Region (hg38): 7:44200958-44214294

Links

ENSG00000106636 ∙ NCBI:10652 ∙ OMIM:606209 ∙ HGNC:16959 ∙ Uniprot:O15498 ∙ 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 YKT6 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YKT6 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in YKT6

This is a list of pathogenic ClinVar variants found in the YKT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-44201154-A-G		not specified	Uncertain significance (Apr 07, 2023)
7-44204615-C-T		not specified	Uncertain significance (Oct 10, 2023)
7-44204647-C-A		not specified	Uncertain significance (Sep 13, 2023)
7-44206388-A-G		not specified	Uncertain significance (Sep 28, 2021)
7-44208146-C-T		not specified	Uncertain significance (Feb 05, 2024)
7-44211027-A-C		not specified	Uncertain significance (Jul 13, 2021)
7-44211086-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YKT6	protein_coding	protein_coding	ENST00000223369	7	13327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.362	0.636	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.986	84	114	0.740	0.00000630	1283
Missense in Polyphen		13	21.033	0.61809		267
Synonymous	0.447	41	44.8	0.915	0.00000252	382
Loss of Function	2.61	3	13.3	0.226	7.46e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Vesicular soluble NSF attachment protein receptor (v- SNARE) mediating vesicle docking and fusion to a specific acceptor cellular compartment. Functions in endoplasmic reticulum to Golgi transport; as part of a SNARE complex composed of GOSR1, GOSR2 and STX5. Functions in early/recycling endosome to TGN transport; as part of a SNARE complex composed of BET1L, GOSR1 and STX5. Has a S-palmitoyl transferase activity. {ECO:0000269|PubMed:15215310, ECO:0000269|PubMed:9211930}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.167
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.765
• ghis: 0.609

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ykt6

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle targeting;vesicle docking involved in exocytosis;protein transport;retrograde transport, endosome to Golgi;membrane fusion
• Cellular component: Golgi membrane;cytoplasm;mitochondrion;endosome;endoplasmic reticulum;Golgi apparatus;cytosol;integral component of plasma membrane;transport vesicle;cytoplasmic vesicle membrane;SNARE complex;endoplasmic reticulum-Golgi intermediate compartment membrane;neuronal cell body;apical dendrite;basal dendrite
• Molecular function: SNAP receptor activity;protein-cysteine S-palmitoyltransferase activity;cadherin binding