GDPD4

Chr 11

glycerophosphodiester phosphodiesterase domain containing 4

Also known as: GDE6, ugpQ

NCBI Gene: 220032 ENSG00000178795 UniProt: Q6W3E5

Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in lipid metabolic process. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.11

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.11LOEUF

pLI 0.000

Z-score 1.09

OE 0.78 (0.56–1.11)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.00Z-score

OE missense 1.00 (0.91–1.10)

272 obs / 272.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.78 (0.56–1.11)

0≤0.351.4

Missense OE?1.00 (0.91–1.10)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 23 / 29.4Missense obs/exp: 272 / 272.1Syn Z: 0.44

Background carrier burden — how many people carry a rare variant somewhere in GDPD4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 73

797 rare PASS variants

Rare truncating (LoF)

1 in 150

173 rare PASS variants

Rare synonymous (reference)

1 in 240

281 rare PASS variants

Rare missense and truncating variants are carried at similar rates in GDPD4; this gene does not show strong loss-of-function constraint by this measure. 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 140	1 in 240
South Asian	~43k	1 in 49	1 in 200
Remaining (unassigned)	~30k	1 in 69	1 in 130
European (Finnish)	~27k	1 in 180	1 in 1,600
Admixed American	~22k	1 in 61	1 in 220
African / African American	~21k	1 in 57	1 in 360
East Asian	~20k	1 in 99	1 in 520
Ashkenazi Jewish	~13k	1 in 400	1 in 420
Middle Eastern	~2,884	1 in 44	1 in 120

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 12 of 15 coding exons well covered in gnomAD exomes; exons 8, 15, 17 marginal. Genomes: all 15.? see exons ↓