What condition is associated with EDAR c.1024+16del?

EDAR c.1024+16del is associated with ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant, autosomal recessive hypohidrotic ectodermal dysplasia (ClinVar).

EDAR c.1024+16del

Q: Is EDAR c.1024+16del pathogenic?

EDAR c.1024+16del is classified Benign in EDAR (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-04). Common (popmax 50.4%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant.

Q: How common is EDAR c.1024+16del in the general population?

EDAR c.1024+16del is common (popmax 50.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs3833574 · VCV155863

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 50.4%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +16	near-intronic (+16 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.9	GERP -2.7
Overall
CADD	0.035	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 50.4% African / African-American · 37,781/74,924 alleles

Filtering AF 50% ClinGen BA1/BS1 input FAF95, joint · FAF99 49.8%

Overall 9.84% 158,438/1,610,286 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	50.4%	2
South Asian	22.1%	5
Middle Eastern	14.2%	7
East Asian	11.4%	9
Remaining individualsnot grpmax-eligible	11.1%	9
Admixed American	7.69%	13
European (non-Finnish)	6.78%	15
Amishnot grpmax-eligible	5.92%	17
Ashkenazi Jewishnot grpmax-eligible	5.71%	18
Finnishnot grpmax-eligible	2.22%	45

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: EDAR
Coding: c.1024+16del
MANE Select: NM_022336
dbSNP: rs3833574
Type: Deletion
Location: chr2:108906292 (GRCh38)
Gene constraint: LOEUF 0.927 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.01 · 1 PDB

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

Disease context

ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive hypohidrotic ectodermal dysplasia

Similar variants

EDAR p.Asp253fs Pathogenic ★ same condition
EDAR p.Glu311fs Pathogenic ★ same condition
EDAR p.Gly390fs Pathogenic ★ same condition
EDAR p.Leu397_Phe398insTer Pathogenic ★ same condition
EDAR p.Leu412fs Likely pathogenic ★ same condition
EDAR p.Lys328fs Pathogenic ★ same condition
EDAR p.Ser407fs Pathogenic ★ same condition
EDAR p.Tyr364fs 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-c-1024-plus-16del (accessed [today's date]).

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