YKT6
Basic information
Region (hg38): 7:44200959-44214294
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 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 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:
| 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:
- 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
- Phenotype
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