PHEX p.Val254del
c.758TGG[1] · rs1064796391 · VCV423381
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
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 1.6, phastCons 1 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. 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
- PHEX
- Protein
- p.Val254del
- Coding
- c.758TGG[1]
- MANE Select
- NM_000444
- dbSNP
- rs1064796391
- Type
- Microsatellite
- Location
- chrX:22094008 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 254
- the peptidase m13 domain
Similar variants
- PHEX c.1586_1586+1del Pathogenic ★★ same type
- PHEX p.Lys320del Pathogenic/Likely pathogenic ★★ same type
- PHEX p.Phe560fs Likely pathogenic ★★ same type
- PHEX p.Ser228fs Pathogenic ★★ same type
- PHEX p.Val70fs Pathogenic ★★ same type
- PHEX p.Val74fs Pathogenic ★★ same type
- PHEX c.187+9_187+10del Benign/Likely benign ★★ same type
- PHEX c.436_436+1del 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/phex-p-val254del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown