Is EHMT2 p.Val479= (c.1437G>A) pathogenic?

EHMT2 p.Val479= (c.1437G>A) is classified Benign in EHMT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-12-17). Common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele.

EHMT2 p.Val479=

Q: How common is EHMT2 p.Val479= (c.1437G>A) in the general population?

EHMT2 p.Val479= (c.1437G>A) is common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1437G>A · rs113973079 · VCV1276428

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 10.7%, sas) — too common for a highly-penetrant pathogenic allele

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 -0.76	GERP -5.2, phastCons 0.004
Overall
CADD	5.158	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 10.7% South Asian · 9,744/91,036 alleles

Filtering AF 10.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 10.5%

Overall 2.39% 38,553/1,612,808 alleles · common exomes 35,890/1,460,500 · genomes 2,663/152,308 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	10.7%	9
East Asian	6.19%	16
Remaining individualsnot grpmax-eligible	3.1%	32
Finnishnot grpmax-eligible	1.87%	54
European (non-Finnish)	1.84%	54
Middle Eastern	1.55%	64
Ashkenazi Jewishnot grpmax-eligible	1.19%	84
Amishnot grpmax-eligible	0.768%	130
Admixed American	0.72%	139
African / African-American	0.512%	195

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: EHMT2
Protein: p.Val479=
Coding: c.1437G>A
MANE Select: NM_006709
dbSNP: rs113973079
Type: single nucleotide variant
Location: chr6:31888435 (GRCh38)
Gene constraint: LOEUF 0.492 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 69.25 · 34 PDB

Full EHMT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EHMT2 p.Ala1077Thr Pathogenic ★★ same type
EHMT2 p.Ala1077Ser Pathogenic ★ same type
EHMT2 p.Asn1112Ser Pathogenic ★ ⚠ same type
EHMT2 p.Lys1162Arg Pathogenic ★ same type
EHMT2 p.Phe1158Leu Pathogenic ★ same type
EHMT2 c.328+2T>G Uncertain significance ★ same type
EHMT2 p.Ala137Ser Uncertain significance ★ ⚠ same type
EHMT2 p.Ala17Pro Uncertain significance ★ ⚠ same type

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/ehmt2-p-val479 (accessed [today's date]).

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