ZNF609

Chr 15

zinc finger protein 609

NCBI Gene: 23060 ENSG00000180357 UniProt: O15014 OMIM: 617474

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and promoter-specific chromatin binding activity. Involved in regulation of myoblast proliferation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.15

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.15LOEUF

pLI 1.000

Z-score 6.18

OE 0.06 (0.03–0.15)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.83Z-score

OE missense 0.82 (0.77–0.87)

651 obs / 796.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.06 (0.03–0.15)

0≤0.351.4

Missense OE?0.82 (0.77–0.87)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 3 / 50.3Missense obs/exp: 651 / 796.0Syn Z: -0.29

Background carrier burden — how many people carry a rare variant somewhere in ZNF609?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 43

1,763 rare PASS variants

Rare truncating (LoF)

1 in 5,000

41 rare PASS variants

Rare synonymous (reference)

1 in 46

730 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ZNF609. 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 60	1 in 9,300
South Asian	~43k	1 in 33	≈ 1 in 13,000
Remaining (unassigned)	~30k	1 in 35	1 in 2,600
European (Finnish)	~27k	1 in 140	≈ 1 in 26,000
Admixed American	~22k	1 in 44	≈ 1 in 5,500
African / African American	~21k	1 in 32	1 in 980
East Asian	~20k	1 in 39	1 in 3,200
Ashkenazi Jewish	~13k	1 in 170	none seen
Middle Eastern	~2,884	1 in 34	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): All 8 coding exons well covered in gnomAD exomes and genomes.? see exons ↓