GLYCTK
Basic information
Region (hg38): 3:52287089-52295257
Links
Phenotypes
GenCC
Source:
- D-glyceric aciduria (Supportive), mode of inheritance: AR
- D-glyceric aciduria (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
D-glyceric aciduria | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Neurologic | 4599249; 2537226; 20949620 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYCTK 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 | 36 | 41 | ||||
missense | 87 | 11 | 103 | |||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 7 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 2 | 1 | 5 | ||
non coding | 5 | |||||
Total | 1 | 2 | 94 | 52 | 9 |
Variants in GLYCTK
This is a list of pathogenic ClinVar variants found in the GLYCTK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-52290363-C-T | Benign (Jul 19, 2023) | |||
3-52290370-C-G | Uncertain significance (Nov 27, 2023) | |||
3-52290371-G-T | not specified | Uncertain significance (Jun 03, 2024) | ||
3-52290379-C-T | D-Glyceric aciduria | Conflicting classifications of pathogenicity (Dec 08, 2022) | ||
3-52290380-G-A | not specified | Uncertain significance (May 08, 2023) | ||
3-52290385-C-T | not specified | Uncertain significance (May 14, 2024) | ||
3-52290392-A-G | not specified | Likely benign (Nov 13, 2023) | ||
3-52290394-C-T | Uncertain significance (Mar 26, 2022) | |||
3-52290399-C-T | Likely benign (Aug 17, 2023) | |||
3-52290401-TCTG-T | D-Glyceric aciduria | Uncertain significance (Dec 18, 2017) | ||
3-52290406-C-T | Uncertain significance (Aug 12, 2022) | |||
3-52290413-C-T | Likely benign (Sep 20, 2021) | |||
3-52290421-C-T | Benign (Jan 15, 2024) | |||
3-52290422-G-A | Likely benign (Nov 25, 2023) | |||
3-52290454-G-A | D-Glyceric aciduria | Uncertain significance (Jan 01, 2016) | ||
3-52290472-A-G | Uncertain significance (May 08, 2023) | |||
3-52290494-C-T | Uncertain significance (Jun 13, 2022) | |||
3-52290495-G-A | GLYCTK-related disorder | Likely benign (Oct 01, 2022) | ||
3-52290511-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
3-52290514-G-C | not specified | Uncertain significance (Nov 07, 2022) | ||
3-52290519-A-G | Likely benign (Oct 24, 2022) | |||
3-52290528-C-T | Likely benign (Aug 01, 2022) | |||
3-52290536-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
3-52290553-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
3-52290559-C-T | Uncertain significance (Jun 22, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GLYCTK | protein_coding | protein_coding | ENST00000436784 | 4 | 8168 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
9.65e-11 | 0.0453 | 125681 | 0 | 61 | 125742 | 0.000243 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.228 | 333 | 322 | 1.04 | 0.0000200 | 3298 |
Missense in Polyphen | 84 | 83.288 | 1.0086 | 906 | ||
Synonymous | -0.502 | 147 | 139 | 1.05 | 0.00000777 | 1232 |
Loss of Function | -0.171 | 15 | 14.3 | 1.05 | 6.14e-7 | 154 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000917 | 0.000915 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000111 | 0.000109 |
Finnish | 0.0000466 | 0.0000462 |
European (Non-Finnish) | 0.000212 | 0.000211 |
Middle Eastern | 0.000111 | 0.000109 |
South Asian | 0.000263 | 0.000261 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Familial lipoprotein lipase deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Glycerolipid Metabolism;Glycerol Kinase Deficiency;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;D-glyceric acidura;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Fructose metabolism;Metabolism of carbohydrates;Metabolism;Fructose catabolism
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.810
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 69.46
Haploinsufficiency Scores
- pHI
- 0.0397
- hipred
- N
- hipred_score
- 0.177
- ghis
- 0.383
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.766
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Glyctk
- Phenotype
Gene ontology
- Biological process
- protein phosphorylation;fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
- Cellular component
- cytoplasm;mitochondrion;Golgi apparatus;cytosol
- Molecular function
- protein binding;ATP binding;glycerate kinase activity