PHEX p.Gln383=
c.1149G>A · rs779998335 · VCV2961758
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00874%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.011 | GERP -3.2, phastCons 0.18 |
| Overall | ||
| CADD | 2.991 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00874%
Admixed American · 4/45,784 alleles
Filtering AF
0.00294%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00177%
Overall
0.000583%
7/1,200,972 alleles · very rare
exomes 5/1,088,506 · genomes 2/112,466 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00874% | 11,446 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,297 |
| South Asian | 0.00177% | 56,647 |
| African / African-American | 0.00175% | 57,168 |
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.Gln383=
- Coding
- c.1149G>A
- MANE Select
- NM_000444
- dbSNP
- rs779998335
- Type
- single nucleotide variant
- Location
- chrX:22111536 (GRCh38)
- Structure
- AlphaFold pLDDT 94.58
- Residue 383
- the peptidase m13 domain
Similar variants
- PHEX p.Gln383Ter Pathogenic ★★ same residue
- PHEX p.Gln383Arg Uncertain significance ★ ⚠ same residue
- PHEX p.Gln383fs 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
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-gln383 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown