PHYH p.Pro74=
c.222T>A · rs1030341153 · VCV2829835
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,552,482)
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 -0.15 | GERP -3.5, phastCons 0.003 |
| Overall | ||
| CADD | 0.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,552,482). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PHYH
- Protein
- p.Pro74=
- Coding
- c.222T>A
- MANE Select
- NM_006214
- dbSNP
- rs1030341153
- Type
- single nucleotide variant
- Location
- chr10:13295519 (GRCh38)
- Gene constraint
- LOEUF 1.147 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.33 · 1 PDB
Similar variants
- 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
- PHYH c.678+2T>C Likely pathogenic ★★ same type
- PHYH p.Ala277Glu Pathogenic/Likely pathogenic ★★ same type
- PHYH p.Arg275Gln 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-pro74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown