VKORC1L1
Basic information
Region (hg38): 7:65873073-65959563
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 VKORC1L1 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 | 1 | |||||
| missense | 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 | 1 | 0 |
Variants in VKORC1L1
This is a list of pathogenic ClinVar variants found in the VKORC1L1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-65873516-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 7-65873545-C-T | Likely benign (Dec 01, 2022) | |||
| 7-65954181-T-C | not specified | Uncertain significance (Jun 12, 2023) | ||
| 7-65954187-A-G | not specified | Uncertain significance (Nov 13, 2023) | ||
| 7-65954220-C-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 7-65954262-G-T | Malignant tumor of prostate | Uncertain significance (-) | ||
| 7-65954294-G-T | not specified | Uncertain significance (Dec 14, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VKORC1L1 | protein_coding | protein_coding | ENST00000360768 | 3 | 86297 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.844 | 0.153 | 118022 | 0 | 1 | 118023 | 0.00000424 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.79 | 47 | 96.5 | 0.487 | 0.00000525 | 1093 |
| Missense in Polyphen | 10 | 34.992 | 0.28578 | 456 | ||
| Synonymous | 0.178 | 44 | 45.5 | 0.966 | 0.00000279 | 371 |
| Loss of Function | 2.29 | 0 | 6.12 | 0.00 | 2.59e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000931 | 0.00000931 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in vitamin K metabolism. Can reduce inactive vitamin K 2,3-epoxide to active vitamin K (in vitro), and may contribute to vitamin K-mediated protection against oxidative stress. Plays a role in vitamin K-dependent gamma-carboxylation of Glu residues in target proteins. {ECO:0000269|PubMed:21367861, ECO:0000269|PubMed:23928358, ECO:0000269|PubMed:24532791}.;
- Pathway
- Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human);Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Metabolism of vitamin K
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.0921
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.729
- ghis
- 0.661
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vkorc1l1
- Phenotype
- homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- peptidyl-glutamic acid carboxylation;cellular response to oxidative stress;vitamin K metabolic process;oxidation-reduction process
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
- Molecular function
- vitamin-K-epoxide reductase (warfarin-sensitive) activity;quinone binding