Is EDAR p.Arg420Gln (c.1259G>A) pathogenic?

EDAR p.Arg420Gln (c.1259G>A) is classified Pathogenic/Likely pathogenic in EDAR (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-06). AlphaMissense: likely pathogenic (0.9575); Absent from gnomAD v4.1; Associated with EDAR-related disorder.

How common is EDAR p.Arg420Gln (c.1259G>A) in the general population?

EDAR p.Arg420Gln (c.1259G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EDAR p.Arg420Gln (c.1259G>A)?

AlphaMissense predicts likely pathogenic (score 0.9575) — an in-silico prediction, not a clinical call.

EDAR p.Arg420Gln

Q: What condition is associated with EDAR p.Arg420Gln (c.1259G>A)?

EDAR p.Arg420Gln (c.1259G>A) is associated with EDAR-related disorder, ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant, ectodermal dysplasia 11B, hypohidrotic/hair/tooth type, autosomal recessive (ClinVar).

c.1259G>A · rs121908453 · VCV5853

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

AlphaMissense

likely pathogenic

0.9575 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

EDAR-related disorder

Computational evidence

Protein change
AlphaMissense	0.9575	likely pathogenic ✓ concordant with ClinVar
REVEL	0.733	pathogenic-leaning
SaProt	LLR -10.36	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 0.91, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 34 kb · p 0.0061 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: EDAR
Protein: p.Arg420Gln
Coding: c.1259G>A
MANE Select: NM_022336
dbSNP: rs121908453
Type: single nucleotide variant
Location: chr2:108896995 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.01 · 1 PDB
Residue 420: a UniProt-annotated variant site (in ectd10a and ectd10b; abolishes nf-kappa-b activation and reduces jnk activation); the death domain

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

Disease context

EDAR-related disorder

Also linked: ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant ectodermal dysplasia 11B, hypohidrotic/hair/tooth type, autosomal recessive autosomal recessive hypohidrotic ectodermal dysplasia

Similar variants

EDAR p.Arg420Trp Likely pathogenic ★ same residue
EDAR p.Ala26Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
EDAR p.Arg25Ter Pathogenic/Likely pathogenic ★★ same condition
EDAR p.Arg358Ter Pathogenic ★★ same condition
EDAR p.Arg89His Pathogenic/Likely pathogenic ★★ ⚠ same condition
EDAR p.Arg98Trp Pathogenic/Likely pathogenic ★★ same condition
EDAR p.Cys301Ter Pathogenic ★★ same condition
EDAR p.Cys428Arg Pathogenic/Likely pathogenic ★★ 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/edar-p-arg420gln (accessed [today's date]).

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