Is EDA c.526+5G>T pathogenic?

EDA c.526+5G>T is classified Likely pathogenic in EDA (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-06-12). Absent from gnomAD v4.1; Associated with EDA-related disorder.

What condition is associated with EDA c.526+5G>T?

EDA c.526+5G>T is associated with EDA-related disorder, X-linked hypohidrotic ectodermal dysplasia (ClinVar).

How common is EDA c.526+5G>T in the general population?

EDA c.526+5G>T is absent from gnomAD v4.1 (gnomAD).

EDA c.526+5G>T

rs397516664 · VCV44196

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EDA-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
Splice region	donor +5	donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	Δ0.82	donor loss · deltas
Pangolin	Δ0.67	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 10	GERP 4.4, phastCons 1
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained
Overall
CADD	16.58	PHRED · no single calibrated threshold — expert panels disagree

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: EDA
Coding: c.526+5G>T
MANE Select: NM_001399
dbSNP: rs397516664
Type: single nucleotide variant
Location: chrX:70023246 (GRCh38)
Structure: AlphaFold pLDDT 70.59 · 3 PDB

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

Disease context

EDA-related disorder

Also linked: X-linked hypohidrotic ectodermal dysplasia

Similar variants

EDA c.526+2T>C Pathogenic/Likely pathogenic ★★ same condition
EDA c.527-2A>G Pathogenic/Likely pathogenic ★★ same condition
EDA c.706+1G>A Pathogenic/Likely pathogenic ★★ same condition
EDA c.707-13T>G Pathogenic ★★ same condition
EDA c.742-2A>G Pathogenic/Likely pathogenic ★★ same condition
EDA c.924+1G>T Likely pathogenic ★★ same condition
EDA p.Ala349Ser Likely pathogenic ★★ same condition
EDA p.Ala349Thr 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/eda-c-526-plus-5g-t (accessed [today's date]).

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