Is ETV6 p.Ser22= (c.66C>T) pathogenic?

ETV6 p.Ser22= (c.66C>T) is classified Likely benign in ETV6 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-21). Very rare (popmax 0.00441%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ETV6 p.Ser22= (c.66C>T)?

ETV6 p.Ser22= (c.66C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ETV6 p.Ser22= (c.66C>T) in the general population?

ETV6 p.Ser22= (c.66C>T) is very rare (popmax 0.00441%, nfe) (gnomAD).

ETV6 p.Ser22=

c.66C>T · VCV3846440

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00441%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 0.9, phastCons 1
Overall
CADD	9.585	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00441% European (non-Finnish) · 52/1,179,932 alleles

Filtering AF 0.00342% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.00359% 58/1,613,798 alleles · very rare exomes 52/1,461,632 · genomes 6/152,166 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00441%	22,691
Finnishnot grpmax-eligible	0.00313%	31,966
African / African-American	0.00267%	37,447
Admixed American	0.00167%	60,000
Remaining individualsnot grpmax-eligible	0.0016%	62,474

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: ETV6
Protein: p.Ser22=
Coding: c.66C>T
MANE Select: NM_001987
Type: single nucleotide variant
Location: chr12:11752482 (GRCh38)
Gene constraint: LOEUF 0.44 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 62.61 · 43 PDB
Residue 22: a modified residue (phosphoserine); the 'disordered' region; a turn

Full ETV6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ETV6 p.Ser22Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
ETV6 p.Arg359Ter Pathogenic ★★ same condition
ETV6 p.Arg369Gln Pathogenic/Likely pathogenic ★★ same condition
ETV6 c.1010-3T>C Uncertain significance ★★ same condition
ETV6 p.Ala247Gly Uncertain significance ★★ ⚠ same condition
ETV6 p.Ala67Asp Uncertain significance ★★ ⚠ same condition
ETV6 p.Ala73Ser Uncertain significance ★★ ⚠ same condition
ETV6 p.Arg127Trp Uncertain significance ★★ ⚠ same condition

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/etv6-p-ser22 (accessed [today's date]).

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