PHEX p.Thr679=
c.2037C>T · rs766459849 · VCV2084984
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.184%, 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 1.1 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 15.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.184%
South Asian · 104/56,634 alleles
Filtering AF
0.155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.144%
Overall
0.00939%
113/1,203,124 alleles · rare
exomes 102/1,091,348 · genomes 11/111,776 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.184% | 545 |
| Middle Eastern | 0.0231% | 4,336 |
| Remaining individualsnot grpmax-eligible | 0.0127% | 7,902 |
| Admixed American | 0.00219% | 45,695 |
| European (non-Finnish) | 0.000112% | 889,031 |
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.Thr679=
- Coding
- c.2037C>T
- MANE Select
- NM_000444
- dbSNP
- rs766459849
- Type
- single nucleotide variant
- Location
- chrX:22227578 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 679
- the peptidase m13 domain
Similar variants
- PHEX p.Thr679fs 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
- PHEX c.1173+2T>C 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-thr679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown