NEK11

Chr 3

NIMA related kinase 11

NCBI Gene: 79858 ENSG00000114670 UniProt: Q8NG66 OMIM: 609779

This gene encodes a member of the never in mitosis gene A family of kinases. The encoded protein localizes to the nucleoli, and may function with NEK2A in the S-phase checkpoint. The encoded protein appears to play roles in DNA replication and response to genotoxic stress. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.22

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.22LOEUF

pLI 0.000

Z-score 0.45

OE 0.92 (0.70–1.22)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.28Z-score

OE missense 1.04 (0.95–1.14)

353 obs / 338.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.92 (0.70–1.22)

0≤0.351.4

Missense OE?1.04 (0.95–1.14)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 34 / 37.0Missense obs/exp: 353 / 338.5Syn Z: 0.53

Background carrier burden — how many people carry a rare variant somewhere in NEK11?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 63

867 rare PASS variants

Rare truncating (LoF)

1 in 510

183 rare PASS variants

Rare synonymous (reference)

1 in 150

249 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NEK11. 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 100	1 in 540
South Asian	~43k	1 in 74	1 in 440
Remaining (unassigned)	~30k	1 in 59	1 in 320
European (Finnish)	~27k	1 in 220	1 in 260
Admixed American	~22k	1 in 56	1 in 700
African / African American	~21k	1 in 55	1 in 280
East Asian	~20k	1 in 71	1 in 740
Ashkenazi Jewish	~13k	1 in 360	≈ 1 in 3,400
Middle Eastern	~2,884	1 in 72	1 in 280

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): 14 of 16 coding exons well covered in gnomAD exomes; exons 6, 10 marginal. Genomes: all 16.? see exons ↓