PHYH p.Gln176=
c.528G>A · rs1157321807 · VCV2101305
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.12 · SpliceAI calls loss · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 13.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,886 alleles
Overall
6.2e-05%
1/1,614,078 alleles · very rare
exomes 0/1,461,868 · genomes 1/152,210 · joint denominator
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
- PHYH
- Protein
- p.Gln176=
- Coding
- c.528G>A
- MANE Select
- NM_006214
- dbSNP
- rs1157321807
- Type
- single nucleotide variant
- Location
- chr10:13288510 (GRCh38)
- Gene constraint
- LOEUF 1.147 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.33 · 1 PDB
- Residue 176
- a UniProt-annotated variant site (in rd); a binding site
Similar variants
- PHYH p.Gln176Arg Uncertain significance ★ ⚠ same residue
- PHYH p.Gln176Lys Pathogenic same residue
- PHYH p.Gln176fs Likely pathogenic ★ same residue
- PHYH c.134+1G>A Likely pathogenic ★★ same type
- PHYH c.135-1G>C Pathogenic/Likely pathogenic ★★ same type
- PHYH c.135-2A>G Pathogenic ★★ same type
- PHYH c.497-1G>A Likely pathogenic ★★ same type
- PHYH c.497-2A>G Pathogenic/Likely 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/phyh-p-gln176 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown