GK
Basic information
Region (hg38): X:30653359-30731462
Links
Phenotypes
GenCC
Source:
- inborn glycerol kinase deficiency (Definitive), mode of inheritance: AR
- inborn glycerol kinase deficiency (Strong), mode of inheritance: XL
- inborn glycerol kinase deficiency (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Glycerol kinase deficiency | XL | Biochemical | Specific dietary measures (eg, fat/glycerol-restricted diet) can be beneficial | Biochemical; Neurologic | 6325658; 8651297; 9719371; 10736265; 11032329; 18607276; 21542762; 23009783 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (5 variants)
- Inborn glycerol kinase deficiency (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GK 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 | 7 | |||||
missense | 26 | 32 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
splice region | 1 | 1 | ||||
non coding | 25 | 28 | ||||
Total | 7 | 7 | 27 | 7 | 30 |
Highest pathogenic variant AF is 0.000355
Variants in GK
This is a list of pathogenic ClinVar variants found in the GK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-30653592-G-A | Inborn genetic diseases | Uncertain significance (Oct 06, 2023) | ||
X-30653592-G-C | See cases | Uncertain significance (Apr 13, 2023) | ||
X-30653624-G-A | GK-related disorder | Likely benign (Feb 07, 2018) | ||
X-30653779-G-C | Benign (May 12, 2021) | |||
X-30665521-C-A | GK-related disorder | Likely pathogenic (Sep 08, 2023) | ||
X-30665538-C-T | Inborn glycerol kinase deficiency | Uncertain significance (Mar 01, 2022) | ||
X-30665578-G-A | Inborn genetic diseases | Uncertain significance (Jul 29, 2023) | ||
X-30665585-G-C | Inborn genetic diseases • Inborn glycerol kinase deficiency | Likely pathogenic (Jan 17, 2019) | ||
X-30667920-A-C | Benign (May 21, 2021) | |||
X-30668024-G-A | Inborn genetic diseases | Benign (Oct 29, 2019) | ||
X-30668045-T-C | GK-related disorder | Benign (Dec 31, 2019) | ||
X-30668056-A-C | Inborn glycerol kinase deficiency | Uncertain significance (Aug 06, 2021) | ||
X-30668064-G-C | Inborn genetic diseases | Uncertain significance (Sep 26, 2024) | ||
X-30668073-T-C | Uncertain significance (Jun 24, 2024) | |||
X-30668094-A-C | Inborn genetic diseases | Uncertain significance (Sep 26, 2023) | ||
X-30668097-A-G | Inborn genetic diseases • GK-related disorder | Conflicting classifications of pathogenicity (Aug 30, 2023) | ||
X-30668107-C-T | Uncertain significance (Apr 17, 2019) | |||
X-30668120-T-C | Pathogenic (Jun 02, 2015) | |||
X-30669373-G-A | Inborn glycerol kinase deficiency | Pathogenic (May 04, 2022) | ||
X-30669375-G-A | GK-related disorder | Likely benign (Mar 02, 2023) | ||
X-30670451-G-T | Benign (Jun 19, 2021) | |||
X-30670598-ATT-A | Benign (Jun 20, 2021) | |||
X-30677388-C-G | Uncertain significance (May 08, 2024) | |||
X-30691149-A-G | Inborn genetic diseases | Uncertain significance (Sep 26, 2023) | ||
X-30691154-TGA-T | Pathogenic (Jun 12, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GK | protein_coding | protein_coding | ENST00000378943 | 20 | 77250 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.989 | 0.0106 | 125687 | 0 | 3 | 125690 | 0.0000119 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.19 | 81 | 211 | 0.383 | 0.0000156 | 3616 |
Missense in Polyphen | 13 | 75.463 | 0.17227 | 1380 | ||
Synonymous | 0.776 | 64 | 72.4 | 0.884 | 0.00000565 | 1040 |
Loss of Function | 4.27 | 3 | 26.9 | 0.112 | 0.00000199 | 445 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000738 | 0.0000738 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000125 | 0.00000880 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Key enzyme in the regulation of glycerol uptake and metabolism.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Familial lipoprotein lipase deficiency;Glycerolipid Metabolism;Glycerol Kinase Deficiency;D-glyceric acidura;Fatty Acid Beta Oxidation;Type II diabetes mellitus;Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;Triglyceride biosynthesis;Triglyceride metabolism;glycerol degradation
(Consensus)
Recessive Scores
- pRec
- 0.444
Intolerance Scores
- loftool
- 0.121
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.616
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.151
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gk
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- glycerol metabolic process;triglyceride metabolic process;phosphorylation;triglyceride biosynthetic process;glycerol catabolic process;glycerol-3-phosphate biosynthetic process
- Cellular component
- cytoplasm;mitochondrion;mitochondrial outer membrane;cytosol;extracellular exosome
- Molecular function
- glycerol kinase activity;protein binding;ATP binding