PHEX p.Pro344=
c.1032G>A · rs1485980861 · VCV3233874
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00218%, amr)
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 -3.6 | GERP -2.9 |
| Overall | ||
| CADD | 0.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00218%
Admixed American · 1/45,817 alleles
Filtering AF
0.000474%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000343%
Overall
0.00091%
11/1,208,194 alleles · very rare
exomes 11/1,095,810 · genomes 0/112,384 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00218% | 45,817 |
| African / African-American | 0.00174% | 57,319 |
| European (non-Finnish) | 0.00101% | 99,238 |
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.Pro344=
- Coding
- c.1032G>A
- MANE Select
- NM_000444
- dbSNP
- rs1485980861
- Type
- single nucleotide variant
- Location
- chrX:22099104 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 344
- the peptidase m13 domain
Similar variants
- PHEX p.Pro344Leu Uncertain significance ★★ same residue
- PHEX p.Pro344_Tyr346del Uncertain significance ★ 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-pro344 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown