Is ETV6 p.Arg299= (c.897G>A) pathogenic?

ETV6 p.Arg299= (c.897G>A) is classified Likely benign in ETV6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-02). Very rare (popmax 0.0022%, sas); Associated with Inborn genetic diseases.

What condition is associated with ETV6 p.Arg299= (c.897G>A)?

ETV6 p.Arg299= (c.897G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ETV6 p.Arg299= (c.897G>A) in the general population?

ETV6 p.Arg299= (c.897G>A) is very rare (popmax 0.0022%, sas) (gnomAD).

ETV6 p.Arg299=

c.897G>A · VCV4020120

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

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 1.9	GERP -0.24, phastCons 1
Overall
CADD	5.613	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,084 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000248% 4/1,613,236 alleles · very rare exomes 4/1,460,920 · genomes 0/152,316 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,542
European (non-Finnish)	0.000169%	590,012

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.Arg299=
Coding: c.897G>A
MANE Select: NM_001987
Type: single nucleotide variant
Location: chr12:11869857 (GRCh38)
Gene constraint: LOEUF 0.44 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 62.61 · 43 PDB

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.Arg299Lys Uncertain significance ★ ⚠ same residue
ETV6 p.Arg299Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
ETV6 p.Arg299Thr Uncertain significance ★ ⚠ 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

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-arg299 (accessed [today's date]).

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