NEK9

Chr 14

NIMA related kinase 9

Also known as: APUG, LCCS10, NC, NERCC, NERCC1

NCBI Gene: 91754 ENSG00000119638 UniProt: Q8TD19

This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein is activated in mitosis and, in turn, activates other family members during mitosis. This protein also mediates cellular processes that are essential for interphase progression. [provided by RefSeq, Jul 2016]

Research

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtLethal congenital contracture syndrome 10

UniProtNevus comedonicus

UniProtArthrogryposis, Perthes disease, and upward gaze palsy

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.86

LOEUF

GOF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.86LOEUF

pLI 0.000

Z-score 2.40

OE 0.65 (0.50–0.86)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

2.50Z-score

OE missense 0.69 (0.64–0.76)

365 obs / 526.7 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.65 (0.50–0.86)

0≤0.351.4

Missense OE?0.69 (0.64–0.76)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 36 / 55.3Missense obs/exp: 365 / 526.7Syn Z: 0.41

Background carrier burden — how many people carry a rare variant somewhere in NEK9?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 64

1,067 rare PASS variants

Rare truncating (LoF)

1 in 370

163 rare PASS variants

Rare synonymous (reference)

1 in 110

483 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NEK9. 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 78	1 in 1,100
South Asian	~43k	1 in 70	1 in 3,200
Remaining (unassigned)	~30k	1 in 53	1 in 510
European (Finnish)	~27k	1 in 210	1 in 5,300
Admixed American	~22k	1 in 59	1 in 1,300
African / African American	~21k	1 in 68	1 in 1,500
East Asian	~20k	1 in 61	1 in 1,700
Ashkenazi Jewish	~13k	1 in 170	1 in 420
Middle Eastern	~2,884	1 in 73	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): 21 of 22 coding exons well covered in gnomAD exomes; exon 5 marginal. Genomes: all 22.? see exons ↓