GK2

glycerol kinase 2, the group of Glycerol kinases

Basic information

Region (hg38): 4:79406361-79408228

Previous symbols: [ "GKP2" ]

Links

ENSG00000196475 ∙ NCBI:2712 ∙ OMIM:600148 ∙ HGNC:4291 ∙ Uniprot:Q14410 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GK2 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			36			36
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in GK2

This is a list of pathogenic ClinVar variants found in the GK2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-79406568-C-T		not specified	Uncertain significance (Jan 28, 2025)
4-79406595-T-A		not specified	Uncertain significance (Jan 28, 2025)
4-79406677-C-T		not specified	Uncertain significance (Jan 16, 2024)
4-79406696-G-A		not specified	Uncertain significance (Mar 01, 2024)
4-79406697-T-C		not specified	Uncertain significance (Nov 09, 2022)
4-79406705-C-T		not specified	Uncertain significance (Jun 17, 2024)
4-79406732-T-C		not specified	Uncertain significance (Jul 14, 2021)
4-79406749-C-A		not specified	Uncertain significance (Mar 06, 2025)
4-79406749-C-T		not specified	Uncertain significance (Nov 10, 2022)
4-79406778-C-G		not specified	Uncertain significance (Oct 07, 2024)
4-79406879-A-G		not specified	Uncertain significance (Oct 07, 2024)
4-79406928-C-T		not specified	Uncertain significance (Aug 10, 2024)
4-79406988-G-A			Likely benign (Jan 11, 2018)
4-79407030-G-A		not specified	Uncertain significance (Sep 11, 2024)
4-79407034-T-A		not specified	Uncertain significance (Jun 10, 2022)
4-79407098-T-C		not specified	Uncertain significance (Aug 27, 2024)
4-79407113-G-C		not specified	Uncertain significance (Dec 17, 2024)
4-79407181-C-G		not specified	Uncertain significance (Oct 04, 2024)
4-79407212-C-T		not specified	Uncertain significance (Jul 14, 2022)
4-79407280-T-A		not specified	Uncertain significance (Oct 25, 2023)
4-79407402-G-T		not specified	Uncertain significance (Jun 14, 2023)
4-79407450-C-T		not specified	Uncertain significance (Jun 05, 2023)
4-79407452-C-T		not specified	Uncertain significance (Feb 08, 2025)
4-79407473-A-T		not specified	Uncertain significance (Dec 03, 2024)
4-79407612-T-C		not specified	Uncertain significance (Jul 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GK2	protein_coding	protein_coding	ENST00000358842	1	1865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-10	0.116	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0516	297	295	1.01	0.0000154	3608
Missense in Polyphen		107	111.08	0.96328		1460
Synonymous	-0.0220	105	105	1.00	0.00000586	1124
Loss of Function	0.275	15	16.2	0.926	8.91e-7	207

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key enzyme in the regulation of glycerol uptake and metabolism. {ECO:0000250}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Fatty Acid Beta Oxidation;Triacylglyceride Synthesis;PPAR signaling pathway;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;Triglyceride biosynthesis;Triglyceride metabolism;glycerol degradation (Consensus)

Intolerance Scores

• loftool: 0.348
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.170
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.836

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gk2

Gene ontology

• Biological process: glycerol metabolic process;triglyceride metabolic process;phosphorylation;glycerol catabolic process;glycerol-3-phosphate biosynthetic process
• Cellular component: cytoplasm;mitochondrion;mitochondrial outer membrane;extracellular exosome
• Molecular function: glycerol kinase activity;ATP binding