ECE1 p.Val171=
c.513G>T · VCV3910070
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.64 | GERP -1.8, phastCons 0.29 |
| Overall | ||
| CADD | 5.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ECE1
- Protein
- p.Val171=
- Coding
- c.513G>T
- MANE Select
- NM_001397
- Type
- single nucleotide variant
- Location
- chr1:21260373 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 91.16 · 1 PDB
- Residue 171
- a disulfide bond; the peptidase m13 domain
Similar variants
- ECE1 p.Thr312Met Uncertain significance ★★ ⚠ same type
- ECE1 c.1020+15G>A Benign ★★ same type
- ECE1 c.1164-5C>T Benign ★★ same type
- ECE1 c.1278+7C>T Benign ★★ same type
- ECE1 c.1782-4C>A Benign ★★ same type
- ECE1 c.828+8T>C Benign ★★ same type
- ECE1 p.Asn397Ser Benign ★★ same type
- ECE1 p.Asp547= Benign ★★ 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/ece1-p-val171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown