EHHADH p.Val40=
c.120A>G · rs566693656 · VCV3052087
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0162%, 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 -0.63 | GERP -2 |
| Overall | ||
| CADD | 0.781 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0162%
European (non-Finnish) · 191/1,179,966 alleles
Filtering AF
0.0143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.0128%
206/1,614,088 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0162% | 6,178 |
| Admixed American | 0.0133% | 7,501 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| South Asian | 0.0022% | 45,527 |
| African / African-American | 0.00133% | 75,066 |
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
- EHHADH
- Protein
- p.Val40=
- Coding
- c.120A>G
- MANE Select
- NM_001966
- dbSNP
- rs566693656
- Type
- single nucleotide variant
- Location
- chr3:185248472 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.07
- Residue 40
- the 'enoyl-coa hydratase / isomerase' region; a UniProt-annotated variant site (in)
Similar variants
- EHHADH p.Val40Ile Uncertain significance ★ ⚠ same residue
- EHHADH p.Ala10Thr Uncertain significance ★★ ⚠ same type
- EHHADH p.Ala118Val Uncertain significance ★★ ⚠ same type
- EHHADH p.Ala294Val Uncertain significance ★★ ⚠ same type
- EHHADH p.Arg183Gly Uncertain significance ★★ ⚠ same type
- EHHADH p.Arg633Cys Uncertain significance ★★ ⚠ same type
- EHHADH p.Arg64Cys Uncertain significance ★★ ⚠ same type
- EHHADH p.Asn629Ser 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/ehhadh-p-val40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown