GLYCTK

glycerate kinase

Basic information

Region (hg38): 3:52287088-52295257

Links

ENSG00000168237 ∙ NCBI:132158 ∙ OMIM:610516 ∙ HGNC:24247 ∙ Uniprot:Q8IVS8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• D-glyceric aciduria (Supportive), mode of inheritance: AR
• D-glyceric aciduria (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the GLYCTK gene.

• 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			1	36	4	41
missense			87	11	5	103
nonsense			1			1
start loss						0
frameshift	1	2	4			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	2	1	5
non coding				5		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: gnomAD

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: dbNSFP

• 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

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