EHD1 p.Ala373=
c.1119G>A · rs749125705 · VCV750340
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0283%, amr)
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 2.9 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 13.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0283%
Admixed American · 17/60,004 alleles
Filtering AF
0.018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00387%
62/1,601,048 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0283% | 3,530 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,201 |
| East Asian | 0.0178% | 5,610 |
| European (non-Finnish) | 0.00212% | 47,195 |
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.Ala373=
- Coding
- c.1119G>A
- MANE Select
- NM_006795
- dbSNP
- rs749125705
- Type
- single nucleotide variant
- Location
- chr11:64854819 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI 0.11 (gnomAD)
- Structure
- AlphaFold pLDDT 89.65 · 5 PDB
Similar variants
- EHD1 p.Ala373Val Uncertain significance ★ ⚠ same residue
- 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.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-ala373 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown