ECHS1 p.Leu193=
c.579C>A · VCV3349860
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,612,576)
Conditions
1
ECHS1-related disorder
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 3.7 | phastCons 1 |
| Overall | ||
| CADD | 8.393 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,612,576). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ECHS1
- Protein
- p.Leu193=
- Coding
- c.579C>A
- MANE Select
- NM_004092
- Type
- single nucleotide variant
- Location
- chr10:133366929 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.54 · 6 PDB
- Residue 193
- an α-helix
Disease context
ECHS1-related disorder
Similar variants
- ECHS1 p.Arg54Cys Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 p.Asn59Ser Pathogenic/Likely pathogenic ★★ same condition
- ECHS1 p.Thr180Ala Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ECHS1 p.Thr277Ile Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ECHS1 c.89-2A>G Likely pathogenic ★ same condition
- ECHS1 p.Gly175Ser Conflicting classifications of pathogenicity ★ ⚠ same condition
- ECHS1 p.Tyr153Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
- ECHS1 c.286+4C>A Likely benign 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-leu193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown