ETV3

Chr 1

ETS variant transcription factor 3

Also known as: METS, PE-1, PE1

NCBI Gene: 2117 ENSG00000117036 UniProt: P41162 OMIM: 164873

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be part of RNA polymerase II transcription repressor complex. Predicted to be active in nucleus. [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

0.30

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.30LOEUF

pLI 0.976

Z-score 3.46

OE 0.06 (0.02–0.30)

Highly constrained

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

Missense Constraint?

2.30Z-score

OE missense 0.62 (0.55–0.70)

185 obs / 296.3 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.06 (0.02–0.30)

0≤0.351.4

Missense OE?0.62 (0.55–0.70)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 1 / 15.9Missense obs/exp: 185 / 296.3Syn Z: 0.12

Background carrier burden — how many people carry a rare variant somewhere in ETV3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

534 rare PASS variants

Rare truncating (LoF)

1 in 13,000

24 rare PASS variants

Rare synonymous (reference)

1 in 160

238 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ETV3. 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 190	1 in 15,000
South Asian	~43k	1 in 100	1 in 8,100
Remaining (unassigned)	~30k	1 in 96	≈ 1 in 15,000
European (Finnish)	~27k	1 in 290	≈ 1 in 25,000
Admixed American	~22k	1 in 140	≈ 1 in 21,000
African / African American	~21k	1 in 120	1 in 2,800
East Asian	~20k	1 in 140	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 1,600	none seen
Middle Eastern	~2,884	1 in 120	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 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓