Is ETV4 p.Ser183= (c.549C>T) pathogenic?

ETV4 p.Ser183= (c.549C>T) is classified Likely benign in ETV4 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-10). Ultra-rare (popmax 0.0168%, sas).

How common is ETV4 p.Ser183= (c.549C>T) in the general population?

ETV4 p.Ser183= (c.549C>T) is ultra-rare (popmax 0.0168%, sas) (gnomAD).

ETV4 p.Ser183=

c.549C>T · rs541926936 · VCV739778

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0168%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.92	GERP -2.4, phastCons 0.2
Overall
CADD	18.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0168% South Asian · 14/83,504 alleles

Filtering AF 0.0101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00808%

Overall 0.00166% 26/1,562,856 alleles · ultra-rare exomes 20/1,410,842 · genomes 6/152,014 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0168%	5,965
East Asian	0.00452%	22,146
African / African-American	0.00137%	73,238
European (non-Finnish)	0.00078%	128,265

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ETV4
Protein: p.Ser183=
Coding: c.549C>T
MANE Select: NM_001079675
dbSNP: rs541926936
Type: single nucleotide variant
Location: chr17:43532936 (GRCh38)

Full ETV4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/etv4-p-ser183 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown