PHEX p.Val717=
c.2151C>G · rs772854418 · VCV1168356
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0195%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.282 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -0.18, phastCons 1 |
| Overall | ||
| CADD | 5.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0195%
South Asian · 11/56,411 alleles
Filtering AF
0.0109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00841%
Overall
0.0011%
13/1,186,077 alleles · ultra-rare
exomes 13/1,072,597 · genomes 0/113,480 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0195% | 5,128 |
| Admixed American | 0.00435% | 22,982 |
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
- PHEX
- Protein
- p.Val717=
- Coding
- c.2151C>G
- MANE Select
- NM_000444
- dbSNP
- rs772854418
- Type
- single nucleotide variant
- Location
- chrX:22247854 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 717
- the peptidase m13 domain
Similar variants
- PHEX p.Val717Gly Likely pathogenic ★ same residue
- PHEX p.Val717Phe Pathogenic ★ same residue
- PHEX c.1079+1G>A Pathogenic ★★ same type
- PHEX c.1079+2T>G Pathogenic ★★ same type
- PHEX c.1080-1G>A Pathogenic ★★ same type
- PHEX c.1080-2A>G Pathogenic ★★ same type
- PHEX c.1080-3C>G Pathogenic ★★ same type
- PHEX c.1173+1G>A 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-val717 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown