Is EDAR p.Ala260Val (c.779C>T) pathogenic?

EDAR p.Ala260Val (c.779C>T) is classified Uncertain significance in EDAR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-24). AlphaMissense: likely benign (0.0842); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EDAR p.Ala260Val (c.779C>T)?

EDAR p.Ala260Val (c.779C>T) is associated with Inborn genetic diseases (ClinVar).

How common is EDAR p.Ala260Val (c.779C>T) in the general population?

EDAR p.Ala260Val (c.779C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EDAR p.Ala260Val (c.779C>T)?

AlphaMissense predicts likely benign (score 0.0842) — an in-silico prediction, not a clinical call.

EDAR p.Ala260Val

c.779C>T · rs2470661488 · VCV2539818

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0842 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0842	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -6.24	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP 2.3, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 34 kb · p 0.0061 · regional, not allelic
Overall
CADD	20.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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.Ala260Val
Coding: c.779C>T
MANE Select: NM_022336
dbSNP: rs2470661488
Type: single nucleotide variant
Location: chr2:108910484 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.01 · 1 PDB
Residue 260: the 'disordered' region

Full EDAR 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

EDAR p.Ala26Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
EDAR p.Glu35Lys Uncertain significance ★★ ⚠ same condition
EDAR p.Gly321Arg Uncertain significance ★★ ⚠ same condition
EDAR p.Ala174Val Uncertain significance ★ ⚠ same condition
EDAR p.Ala217Ser Uncertain significance ★ ⚠ same condition
EDAR p.Ala423Thr Uncertain significance ★ ⚠ same condition
EDAR p.Ala99Thr Uncertain significance ★ ⚠ same condition
EDAR p.Arg282Gln 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/edar-p-ala260val (accessed [today's date]).

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