PHEX p.Thr193=
c.579G>A · rs781542537 · VCV2981449
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, mid)
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 -1.8 | GERP -2.9 |
| Overall | ||
| CADD | 0.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Middle Eastern · 1/4,376 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000689%
Overall
0.000992%
12/1,209,193 alleles · ultra-rare
exomes 11/1,097,650 · genomes 1/111,543 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0229% | 4,376 |
| East Asian | 0.00593% | 16,876 |
| South Asian | 0.00528% | 18,933 |
| African / African-American | 0.0035% | 28,535 |
| Admixed American | 0.00219% | 45,669 |
| European (non-Finnish) | 0.000335% | 298,251 |
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.Thr193=
- Coding
- c.579G>A
- MANE Select
- NM_000444
- dbSNP
- rs781542537
- Type
- single nucleotide variant
- Location
- chrX:22077618 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 193
- the peptidase m13 domain
Similar variants
- PHEX p.Thr193Met Likely benign ★ same residue
- PHEX p.Thr193fs 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-thr193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown