ECHS1 p.Pro163=
c.489G>A · rs140410716 · VCV385034
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | |
| Overall | ||
| CADD | 0.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.05% | 95 |
| Remaining individualsnot grpmax-eligible | 0.125% | 801 |
| South Asian | 0.0637% | 1,570 |
| Middle Eastern | 0.033% | 3,030 |
| Admixed American | 0.0283% | 3,530 |
| African / African-American | 0.004% | 25,009 |
| European (non-Finnish) | 0.00186% | 53,633 |
| Finnishnot grpmax-eligible | 0.00157% | 63,738 |
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
- ECHS1
- Protein
- p.Pro163=
- Coding
- c.489G>A
- MANE Select
- NM_004092
- dbSNP
- rs140410716
- Type
- single nucleotide variant
- Location
- chr10:133368948 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.54 · 6 PDB
- Residue 163
- an α-helix
Disease context
mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Mitochondrial short-chain enoyl-CoA hydratase 1 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- ECHS1 p.Pro163Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- ECHS1 p.Pro163Thr Uncertain significance ★ ⚠ same residue
- ECHS1 c.414+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 c.88+5G>A Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 p.Ala132Thr Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 p.Ala173Val Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 p.Ala238Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ECHS1 p.Ala278Thr Likely pathogenic ★★ same condition
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/echs1-p-pro163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown