Is ETV6 p.Asp111= (c.333T>C) pathogenic?

ETV6 p.Asp111= (c.333T>C) is classified Likely benign in ETV6 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-06). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ETV6 p.Asp111= (c.333T>C)?

ETV6 p.Asp111= (c.333T>C) is associated with Inborn genetic diseases (ClinVar).

How common is ETV6 p.Asp111= (c.333T>C) in the general population?

ETV6 p.Asp111= (c.333T>C) is absent from gnomAD v4.1 (gnomAD).

ETV6 p.Asp111=

c.333T>C · rs2497981904 · VCV2769607

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.61	GERP 0.41, phastCons 0.055
Overall
CADD	5.998	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ETV6
Protein: p.Asp111=
Coding: c.333T>C
MANE Select: NM_001987
dbSNP: rs2497981904
Type: single nucleotide variant
Location: chr12:11853431 (GRCh38)
Gene constraint: LOEUF 0.44 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 62.61 · 43 PDB
Residue 111: the pnt domain; an α-helix

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.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
ETV6 p.Arg14Gln 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-asp111 (accessed [today's date]).

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