PHEX p.Arg567=
c.1701A>C · rs2518659982 · VCV2506512
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
X-linked dominant hypophosphatemic rickets
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.33 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.7 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 14.01 | 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
- PHEX
- Protein
- p.Arg567=
- Coding
- c.1701A>C
- MANE Select
- NM_000444
- dbSNP
- rs2518659982
- Type
- single nucleotide variant
- Location
- chrX:22219036 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 567
- the peptidase m13 domain; a UniProt-annotated variant site (in xlhrd)
Disease context
X-linked dominant hypophosphatemic rickets — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor X-linked hypophosphatemia (Orphanet):
- Inheritance
- X-linked dominant
- Onset
- Childhood, Infancy
- Prevalence
- 1-9 / 100 000 (Norway)
Similar variants
- PHEX p.Arg567Ter Pathogenic ★★ same residue
- PHEX p.Arg567Gln Likely benign ★ ⚠ same residue
- PHEX p.Arg567Pro Pathogenic/Likely pathogenic ★★ ⚠ same residue
- PHEX c.1079+1G>A Pathogenic ★★ same condition
- PHEX c.1079+2T>G Pathogenic ★★ same condition
- PHEX c.1080-1G>A Pathogenic ★★ same condition
- PHEX c.1080-3C>G Pathogenic ★★ same condition
- PHEX c.1173+1G>A Pathogenic ★★ 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/phex-p-arg567 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown