GK5

Chr 3

glycerol kinase 5

NCBI Gene: 256356 ENSG00000175066 UniProt: Q6ZS86 OMIM: 620801

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.53

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.53LOEUF

pLI 0.006

Z-score 3.62

OE 0.31 (0.19–0.53)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.95Z-score

OE missense 0.66 (0.58–0.75)

175 obs / 263.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.31 (0.19–0.53)

0≤0.351.4

Missense OE?0.66 (0.58–0.75)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 10 / 32.1Missense obs/exp: 175 / 263.9Syn Z: -0.12

Background carrier burden — how many people carry a rare variant somewhere in GK5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

567 rare PASS variants

Rare truncating (LoF)

1 in 1,300

95 rare PASS variants

Rare synonymous (reference)

1 in 200

243 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GK5. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 330	1 in 1,300
South Asian	~43k	1 in 170	1 in 2,100
Remaining (unassigned)	~30k	1 in 240	1 in 4,900
European (Finnish)	~27k	1 in 290	1 in 3,700
Admixed American	~22k	1 in 150	1 in 1,600
African / African American	~21k	1 in 140	1 in 1,200
East Asian	~20k	1 in 150	1 in 1,200
Ashkenazi Jewish	~13k	1 in 760	1 in 1,700
Middle Eastern	~2,884	1 in 130	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 16 coding exons well covered in gnomAD exomes; exons 2, 3, 4, 7, 8 and 4 more marginal. Genomes: all 16.? see exons ↓