NUDT16

Chr 3

nudix hydrolase 16

NCBI Gene: 131870 ENSG00000198585 UniProt: Q96DE0 OMIM: 617381

Enables several functions, including RNA binding activity; metal ion binding activity; and pyrophosphatase activity. Involved in RNA metabolic process and positive regulation of cell cycle process. Located in cytoplasm; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.90

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.90LOEUF

pLI 0.005

Z-score -0.30

OE 1.21 (0.49–1.90)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.30Z-score

OE missense 0.93 (0.80–1.08)

121 obs / 130.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.21 (0.49–1.90)

0≤0.351.4

Missense OE?0.93 (0.80–1.08)

0≤0.61.4

Synonymous OE?0.87

0≤1.21.6

LoF obs/exp: 3 / 2.5Missense obs/exp: 121 / 130.7Syn Z: 0.79

Background carrier burden — how many people carry a rare variant somewhere in NUDT16?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

463 rare PASS variants

Rare truncating (LoF)

1 in 1,400

79 rare PASS variants

Rare synonymous (reference)

1 in 380

188 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NUDT16. 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 310	1 in 830
South Asian	~43k	1 in 190	1 in 950
Remaining (unassigned)	~30k	1 in 190	1 in 1,600
European (Finnish)	~27k	1 in 240	1 in 880
Admixed American	~22k	1 in 140	1 in 450
African / African American	~21k	1 in 120	1 in 890
East Asian	~20k	1 in 180	1 in 630
Ashkenazi Jewish	~13k	≈ 1 in 13,000	none seen
Middle Eastern	~2,884	1 in 110	≈ 1 in 1,200

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): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓