Is EDA p.Ser160Arg (c.480C>G) pathogenic?

EDA p.Ser160Arg (c.480C>G) is classified Uncertain significance in EDA (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-06). AlphaMissense: likely pathogenic (0.8533); Absent from gnomAD v4.1; Associated with tooth agenesis, selective, X-linked, 1.

What condition is associated with EDA p.Ser160Arg (c.480C>G)?

EDA p.Ser160Arg (c.480C>G) is associated with tooth agenesis, selective, X-linked, 1 (ClinVar).

How common is EDA p.Ser160Arg (c.480C>G) in the general population?

EDA p.Ser160Arg (c.480C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EDA p.Ser160Arg (c.480C>G)?

AlphaMissense predicts likely pathogenic (score 0.8533) — an in-silico prediction, not a clinical call.

EDA p.Ser160Arg

c.480C>G · rs2147419234 · VCV1675183

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8533 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

tooth agenesis, selective, X-linked, 1

Computational evidence

Protein change
AlphaMissense	0.8533	likely pathogenic
REVEL	0.377	indeterminate
SaProt	LLR -7.02	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 2.7, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 419 kb · p 2e-10 · regional, not allelic
Overall
CADD	22.6	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: EDA
Protein: p.Ser160Arg
Coding: c.480C>G
MANE Select: NM_001399
dbSNP: rs2147419234
Type: single nucleotide variant
Location: chrX:69957110 (GRCh38)
Structure: AlphaFold pLDDT 70.59 · 3 PDB
Residue 160: a functional site (cleavage; by furin); the 'disordered' region

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

Disease context

tooth agenesis, selective, X-linked, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EDA p.Ser160Asn Pathogenic/Likely pathogenic ★★ ⚠ same residue
EDA p.Arg155Cys Pathogenic ★★ ⚠ same condition
EDA p.Arg156Cys Pathogenic/Likely pathogenic ★★ same condition
EDA p.Arg156His Pathogenic ★★ ⚠ same condition
EDA p.Arg289Cys Pathogenic ★★ same condition
EDA p.Arg289His Pathogenic/Likely pathogenic ★★ ⚠ same condition
EDA p.Gly299Ser Pathogenic/Likely pathogenic ★★ same condition
EDA p.Met1Thr 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-p-ser160arg (accessed [today's date]).

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