FECH p.Pro62=
c.186G>A · rs550820935 · VCV2165530
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0334%, mid)
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 -14 | GERP -3.2 |
| Overall | ||
| CADD | 0.146 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0334%
Middle Eastern · 2/5,990 alleles
Filtering AF
0.00588%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.0013%
21/1,614,046 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0334% | 2,995 |
| Admixed American | 0.005% | 20,006 |
| African / African-American | 0.00267% | 37,515 |
| European (non-Finnish) | 0.0011% | 90,772 |
| South Asian | 0.0011% | 91,080 |
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
- FECH
- Protein
- p.Pro62=
- Coding
- c.186G>A
- MANE Select
- NM_000140
- dbSNP
- rs550820935
- Type
- single nucleotide variant
- Location
- chr18:57580081 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.37 · 25 PDB
- Residue 62
- a UniProt-annotated variant site (in epp1)
Similar variants
- FECH p.Pro62Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- FECH p.Pro62Ser Uncertain significance ★ ⚠ same residue
- FECH c.1137+3A>G Pathogenic/Likely pathogenic ★★ same type
- FECH c.314+2T>G Pathogenic/Likely pathogenic ★★ same type
- FECH c.463+1G>C Pathogenic ★★ same type
- FECH c.598+1G>T Pathogenic ★★ same type
- FECH c.599-2A>G Pathogenic ★★ same type
- FECH c.913-2A>G Likely pathogenic ★★ 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/fech-p-pro62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown