PHEX p.Ala62=
c.186G>A · rs751752229 · VCV2427885
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00359%, sas)
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 -0.97 | GERP -3.5, phastCons 0.004 |
| Overall | ||
| CADD | 9.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00359%
South Asian · 2/55,642 alleles
Filtering AF
0.000596%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000223%
Overall
0.00043%
5/1,162,649 alleles · very rare
exomes 4/1,051,080 · genomes 1/111,569 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00359% | 27,821 |
| Finnishnot grpmax-eligible | 0.00215% | 46,490 |
| European (non-Finnish) | 0.000235% | 426,192 |
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.Ala62=
- Coding
- c.186G>A
- MANE Select
- NM_000444
- dbSNP
- rs751752229
- Type
- single nucleotide variant
- Location
- chrX:22038536 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 62
- the peptidase m13 domain
Similar variants
- PHEX p.Ala62Glu Uncertain significance ★ ⚠ same residue
- PHEX p.Ala62Thr Uncertain significance ★ ⚠ same residue
- PHEX p.Ala62Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- PHEX p.Ala62Lys Likely 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
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-ala62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown