ZNF106

Chr 15

zinc finger protein 106

Also known as: SH3BP3, ZFP106, ZNF474

NCBI Gene: 64397 ENSG00000103994 UniProt: Q9H2Y7

Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Jul 2025]

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

0.40

LOEUF

—

Mechanism

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.40LOEUF

pLI 0.000

Z-score 6.18

OE 0.29 (0.21–0.40)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.11Z-score

OE missense 0.90 (0.85–0.95)

907 obs / 1006.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.29 (0.21–0.40)

0≤0.351.4

Missense OE?0.90 (0.85–0.95)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 25 / 87.3Missense obs/exp: 907 / 1006.0Syn Z: 0.37

Background carrier burden — how many people carry a rare variant somewhere in ZNF106?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 25

2,280 rare PASS variants

Rare truncating (LoF)

1 in 390

195 rare PASS variants

Rare synonymous (reference)

1 in 79

854 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ZNF106. 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 38	1 in 1,900
South Asian	~43k	1 in 30	1 in 510
Remaining (unassigned)	~30k	1 in 23	1 in 710
European (Finnish)	~27k	1 in 71	1 in 2,400
Admixed American	~22k	1 in 28	1 in 1,200
African / African American	~21k	1 in 24	1 in 820
East Asian	~20k	1 in 30	1 in 1,300
Ashkenazi Jewish	~13k	1 in 73	≈ 1 in 4,400
Middle Eastern	~2,884	1 in 32	1 in 480

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): 20 of 21 coding exons well covered in gnomAD exomes; exon 19 marginal. Genomes: all 21.? see exons ↓