# NM_001399.5(EDA):c.632C>G (p.Thr211Arg)

https://sugi.bio/variant/eda-p-thr211arg

## Summary

**EDA p.Thr211Arg (c.632C>G)** is classified **Pathogenic** in EDA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-01). AlphaMissense: likely pathogenic (0.6568); Absent from gnomAD v4.1; Associated with X-linked hypohidrotic ectodermal dysplasia.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2147509853 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the EDA gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to X-linked hypohidrotic ectodermal dysplasia.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Autosomal recessive, X-linked recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Prevalence | 1-9 / 100 000 (Europe) |
| Clinical trials | 14 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | EDA is a diagnostic-grade gene on 4 Genomics England panels |

**Commonly reported features of Hypohidrotic ectodermal dysplasia** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Abnormality of the dentition — Very frequent (99-80%)
- Hypoplasia of the maxilla — Very frequent (99-80%)
- Dry skin — Very frequent (99-80%)
- Thin skin — Very frequent (99-80%)
- Keratoconjunctivitis sicca — Very frequent (99-80%)
- Abnormal facial shape — Very frequent (99-80%)
- Abnormal dental morphology — Very frequent (99-80%)
- Irregular hyperpigmentation — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010427/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [EDA](https://sugi.bio/atlas/gene/EDA/) |
| Protein change (HGVS p.) | p.Thr211Arg |
| Coding change (HGVS c.) | c.632C>G |
| MANE Select transcript | [NM_001399](https://www.ncbi.nlm.nih.gov/nuccore/NM_001399) |
| dbSNP | [rs2147509853](https://www.ncbi.nlm.nih.gov/snp/rs2147509853/) |
| Variant type | single nucleotide variant |
| Location | chrX:70027962-70027962 (GRCh38) |
| ClinVar | [VCV1070895](https://www.ncbi.nlm.nih.gov/clinvar/variation/1070895/) |

**All HGVS expressions:** `NC_000023.10:g.69247812C>G`, `NC_000023.11:g.70027962C>G`, `NG_009809.2:g.416896C>G`, `NM_001005609.2:c.632C>G`, `NM_001005612.3:c.632C>G`, `NM_001399.5:c.632C>G`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.6568) — concordant with the pathogenic call
- REVEL 0.439 (indeterminate)
- SaProt LLR -7.732 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; SaProt does not; REVEL makes no call
- Conservation: phyloP 7.549, GERP 4.36, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 23.3**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.62** across the covering region of the MANE Select transcript (69,616,455–70,035,606), spanning 419,151 bp. Chi-square p 2e-10. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**EDA** population constraint: ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **211** lies in the collagen-like domain; a UniProt-annotated variant site (in xhed); the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 70.59, 38% of residues very-high.

**3 experimental structure(s)** (PDB): [1RJ7](https://www.rcsb.org/structure/1RJ7), [1RJ8](https://www.rcsb.org/structure/1RJ8), [7X9G](https://www.rcsb.org/structure/7X9G).

## What this gene does {#gene-function}

*Describes the biological roles of EDA (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** EDA's established molecular role includes signaling receptor binding. p.Thr211Arg falls in the collagen-like domain.


### Pathways affected {#pathways}

EDA participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [TNFs bind their physiological receptors](https://reactome.org/content/detail/R-HSA-5669034) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** signaling receptor binding, death receptor binding, cytokine activity, death receptor agonist activity.

**Biological process:** cytokine-mediated signaling pathway, odontogenesis of dentin-containing tooth, positive regulation of canonical NF-kappaB signal transduction, regulation of non-canonical NF-kappaB signal transduction.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2020-10-01.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2020-10-01 |

## Associated conditions {#conditions}

[X-linked hypohidrotic ectodermal dysplasia](https://sugi.bio/atlas/disease/x-linked-hypohidrotic-ectodermal-dysplasia/).

**Reported phenotype names (ClinVar):** Hypohidrotic X-linked ectodermal dysplasia, ECTODERMAL DYSPLASIA 1, ECTODERMAL DYSPLASIA 1, HYPOHIDROTIC, X-LINKED, ECTODERMAL DYSPLASIA 1, HYPOHIDROTIC/HAIR/TOOTH TYPE, X-LINKED, Christ-Siemans-Touraine syndrome, Anhidrotic ectodermal dysplasia X-linked, Christ Siemens Touraine syndrome, ECTODERMAL DYSPLASIA, HYPOHIDROTIC, 1, CST SYNDROME, Ectodermal Dysplasia 1, Anhidrotic.

## Similar variants {#similar}

Related EDA variant pages (same residue, condition, or type): [EDA c.526+5G>T](/variant/eda-c-526-plus-5g-t), [EDA c.527-2A>G](/variant/eda-c-527-minus-2a-g), [EDA c.706+1G>A](/variant/eda-c-706-plus-1g-a), [EDA c.707-13T>G](/variant/eda-c-707-minus-13t-g), [EDA c.742-2A>G](/variant/eda-c-742-minus-2a-g), [EDA c.924+1G>T](/variant/eda-c-924-plus-1g-t), [EDA p.Ala349Ser](/variant/eda-p-ala349ser), [EDA p.Ala349Thr](/variant/eda-p-ala349thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1070895). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*