GK5

protein-coding

glycerol kinase 5, the group of Glycerol kinases

Gene summary

Predicted to enable glycerol kinase activity. Predicted to be involved in glycerol metabolic process; glycerol-3-phosphate biosynthetic process; and triglyceride metabolic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001039547.3

Inheritance

—

ClinVar variants

U:34B:5

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr3:142,157,527-142,225,592

External References & Databases

Ensembl (ENSG00000175066)

Transcript & Mutation Effects

hg38 • Region Span ~68.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GK5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039547.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar	5 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	34	5	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039547.3	RefSeq	NP_001034636.1	16	MANE Select
ENST00000392993.7	Ensembl	ENSP00000418001.1	16	MANE Select
ENST00000463349.1	Ensembl	ENSP00000417153.1	2	Standard
ENST00000480757.5	Ensembl	ENSP00000419031.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

CDP-diacylglycerol biosynthesis
glycerol degradation

Biological Process

glycerol metabolic process
triglyceride metabolic process
phosphorylation
glycerol catabolic process
glycerol-3-phosphate biosynthetic process

Molecular Function

glycerol kinase activity
ATP binding

Cellular Component

cytoplasm
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392993
Coding exons: 16
Length: 62036
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.95	175	264	0.663	0.0000122	3472
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00025	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.451
RVIS EVS: -0.58
RVIS percentile EVS: 18.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.271

Gene Damage Prediction

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