FA2H p.Phe11del
c.32_34del · VCV4536231
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.4, phastCons 1 |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.00198% | 50,586 |
| European (non-Finnish)grpmax | 0.00038% | 263,454 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- FA2H
- Protein
- p.Phe11del
- Coding
- c.32_34del
- MANE Select
- NM_024306
- Type
- Deletion
- Location
- chr16:74774722 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.53
- Residue 11
- the cytochrome b5 heme-binding domain
Similar variants
- FA2H p.Phe11Leu Uncertain significance ★ ⚠ same residue
- FA2H c.340_363+8del Pathogenic/Likely pathogenic ★★ same type
- FA2H p.Arg53_Ile58del Pathogenic ★★ same type
- FA2H p.Gly298fs Pathogenic ★★ same type
- FA2H p.Pro44fs Pathogenic ★★ same type
- FA2H p.Thr314fs Pathogenic/Likely pathogenic ★★ same type
- FA2H p.Tyr170_Ser171delinsTer Pathogenic ★★ same type
- FA2H p.Val275fs Pathogenic/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/fa2h-p-phe11del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown