EDNRA p.Cys387=
c.1161C>T · rs2530425942 · VCV2034240
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 18.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
0.000205%
3/1,461,852 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,256 |
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
- EDNRA
- Protein
- p.Cys387=
- Coding
- c.1161C>T
- MANE Select
- NM_001957
- dbSNP
- rs2530425942
- Type
- single nucleotide variant
- Location
- chr4:147542495 (GRCh38)
- Gene constraint
- LOEUF 0.424 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.45 · 5 PDB
Similar variants
- EDNRA p.Gly354Ser Uncertain significance ★★ ⚠ same type
- EDNRA p.His33Arg Uncertain significance ★★ ⚠ same type
- EDNRA p.Ile405Val Uncertain significance ★★ ⚠ same type
- EDNRA p.Ile82Leu Uncertain significance ★★ ⚠ same type
- EDNRA p.Val155Ile Uncertain significance ★★ ⚠ same type
- EDNRA c.1034+19G>A Benign/Likely benign ★★ same type
- EDNRA c.1034+52T>C Benign ★★ same type
- EDNRA c.1035-151G>A Benign ★★ same type
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/ednra-p-cys387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown