NUDCD1

Chr 8

NudC domain containing 1

Also known as: CML66, OVA66

NCBI Gene: 84955 ENSG00000120526 UniProt: Q96RS6 OMIM: 606109

The NUDCD1 protein is predicted to be involved in immune system processes and is located in the cytosol and nucleoplasm. Mutations cause autosomal recessive developmental and epileptic encephalopathy with microcephaly. The gene is not highly constrained against loss-of-function variants, consistent with its recessive inheritance pattern.

OMIM ResearchSummary from RefSeq

Predicted to be involved in immune system process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.01

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.01LOEUF

pLI 0.000

Z-score 1.53

OE 0.70 (0.49–1.01)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.50Z-score

OE missense 0.92 (0.83–1.01)

279 obs / 303.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.70 (0.49–1.01)

0≤0.351.4

Missense OE?0.92 (0.83–1.01)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 21 / 30.1Missense obs/exp: 279 / 303.6Syn Z: 0.39

Background carrier burden — how many people carry a rare variant somewhere in NUDCD1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 72

724 rare PASS variants

Rare truncating (LoF)

1 in 1,100

134 rare PASS variants

Rare synonymous (reference)

1 in 240

241 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NUDCD1. 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 1,000
South Asian	~43k	1 in 78	1 in 640
Remaining (unassigned)	~30k	1 in 79	1 in 1,400
European (Finnish)	~27k	1 in 290	1 in 5,300
Admixed American	~22k	1 in 73	1 in 1,000
African / African American	~21k	1 in 90	1 in 1,700
East Asian	~20k	1 in 78	1 in 890
Ashkenazi Jewish	~13k	1 in 520	1 in 1,200
Middle Eastern	~2,884	1 in 75	≈ 1 in 940

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): 6 of 10 coding exons well covered in gnomAD exomes; exons 2, 4, 5, 8 marginal. Genomes: all 10.? see exons ↓