EHD1 p.Asp436=
c.1308C>T · rs139248473 · VCV780053
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.209%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -3.8 |
| Overall | ||
| CADD | 1.288 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.209%
European (non-Finnish) · 2,467/1,179,936 alleles
Filtering AF
0.202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.199%
Overall
0.165%
2,662/1,613,934 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.209% | 478 |
| Remaining individualsnot grpmax-eligible | 0.136% | 735 |
| Admixed American | 0.105% | 953 |
| Finnishnot grpmax-eligible | 0.0282% | 3,552 |
| African / African-American | 0.02% | 5,002 |
| South Asian | 0.0121% | 8,280 |
| East Asian | 0.00668% | 14,959 |
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
- EHD1
- Protein
- p.Asp436=
- Coding
- c.1308C>T
- MANE Select
- NM_006795
- dbSNP
- rs139248473
- Type
- single nucleotide variant
- Location
- chr11:64854630 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI 0.11 (gnomAD)
- Structure
- AlphaFold pLDDT 89.65 · 5 PDB
Similar variants
- EHD1 p.Ala273= Benign ★★ same type
- EHD1 p.Gly464= Benign ★★ same type
- EHD1 p.Leu114= Benign ★★ same type
- EHD1 p.Leu187= Benign ★★ same type
- EHD1 p.Ala304Gly Uncertain significance ★ ⚠ same type
- EHD1 p.Ala308Thr Uncertain significance ★ ⚠ same type
- EHD1 p.Ala373Val Uncertain significance ★ ⚠ same type
- EHD1 p.Ala413Val Uncertain significance ★ ⚠ 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/ehd1-p-asp436 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown