ZC3H10

Chr 12

zinc finger CCCH-type containing 10

NCBI Gene: 84872 ENSG00000135482 UniProt: Q96K80

Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA

Research

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

0.61

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.61LOEUF

pLI 0.316

Z-score 2.53

OE 0.24 (0.11–0.61)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

2.28Z-score

OE missense 0.61 (0.54–0.69)

165 obs / 270.4 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.24 (0.11–0.61)

0≤0.351.4

Missense OE?0.61 (0.54–0.69)

0≤0.61.4

Synonymous OE?1.15

0≤1.21.6

LoF obs/exp: 3 / 12.7Missense obs/exp: 165 / 270.4Syn Z: -1.17

Background carrier burden — how many people carry a rare variant somewhere in ZC3H10?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 190

390 rare PASS variants

Rare truncating (LoF)

1 in 10,000

32 rare PASS variants

Rare synonymous (reference)

1 in 240

249 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ZC3H10. 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 210	1 in 12,000
South Asian	~43k	1 in 260	≈ 1 in 22,000
Remaining (unassigned)	~30k	1 in 190	≈ 1 in 30,000
European (Finnish)	~27k	1 in 1,200	1 in 3,700
Admixed American	~22k	1 in 260	none seen
African / African American	~21k	1 in 230	≈ 1 in 21,000
East Asian	~20k	1 in 190	none seen
Ashkenazi Jewish	~13k	≈ 1 in 3,300	none seen
Middle Eastern	~2,884	1 in 130	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.