GK5
Basic information
Region (hg38): 3:142157527-142225592
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 GK5 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 | 11 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 5 | 0 |
Variants in GK5
This is a list of pathogenic ClinVar variants found in the GK5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-142165651-G-A | not specified | Uncertain significance (Jun 22, 2023) | ||
| 3-142165680-C-T | not specified | Likely benign (Aug 19, 2024) | ||
| 3-142165699-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
| 3-142170416-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 3-142181508-C-G | not specified | Uncertain significance (Jun 18, 2024) | ||
| 3-142181533-G-C | not specified | Uncertain significance (Feb 17, 2022) | ||
| 3-142182959-T-C | not specified | Likely benign (Oct 27, 2021) | ||
| 3-142186454-T-C | not specified | Likely benign (Jan 03, 2024) | ||
| 3-142187730-G-C | not specified | Uncertain significance (Sep 16, 2021) | ||
| 3-142198827-A-G | not specified | Likely benign (Sep 16, 2021) | ||
| 3-142204793-A-G | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 3-142215620-C-T | not specified | Uncertain significance (Nov 30, 2021) | ||
| 3-142215661-A-T | not specified | Uncertain significance (Aug 04, 2023) | ||
| 3-142225329-A-G | not specified | Likely benign (Dec 04, 2024) | ||
| 3-142225340-G-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 3-142225434-G-A | not specified | Uncertain significance (Nov 21, 2022) | ||
| 3-142225448-C-T | not specified | Uncertain significance (Sep 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GK5 | protein_coding | protein_coding | ENST00000392993 | 16 | 62036 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00634 | 0.994 | 125709 | 0 | 38 | 125747 | 0.000151 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.95 | 175 | 264 | 0.663 | 0.0000122 | 3472 |
| Missense in Polyphen | 64 | 98.052 | 0.65271 | 1338 | ||
| Synonymous | -0.121 | 90 | 88.5 | 1.02 | 0.00000418 | 960 |
| Loss of Function | 3.62 | 10 | 32.1 | 0.311 | 0.00000164 | 380 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000155 | 0.000154 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000266 | 0.000255 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000143 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- CDP-diacylglycerol biosynthesis;glycerol degradation
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.451
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.44
Haploinsufficiency Scores
- pHI
- 0.118
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.271
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gk5
- Phenotype
- immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- glycerol metabolic process;triglyceride metabolic process;phosphorylation;glycerol catabolic process;glycerol-3-phosphate biosynthetic process
- Cellular component
- cytoplasm;mitochondrion
- Molecular function
- glycerol kinase activity;ATP binding