PTRH2 p.Ala56=
c.168A>G · rs142925288 · VCV382976
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.53%, afr)
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 0.33 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 7.047 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.53%
African / African-American · 398/75,046 alleles
Filtering AF
0.487%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.47%
Overall
0.0294%
474/1,614,214 alleles · rare
exomes 223/1,461,892 · genomes 251/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.53% | 189 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.0317% | 3,159 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| European (non-Finnish) | 0.00347% | 28,782 |
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
- PTRH2
- Protein
- p.Ala56=
- Coding
- c.168A>G
- MANE Select
- NM_016077
- dbSNP
- rs142925288
- Type
- single nucleotide variant
- Location
- chr17:59697811 (GRCh38)
- Gene constraint
- LOEUF 1.322 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 1 PDB
Similar variants
- PTH2 p.Thr56Ser Uncertain significance ★ ⚠ same residue
- PTRH2 p.Gln85Pro Pathogenic ★★ same type
- PTRH2 c.1-124A>G Likely benign ★★ same type
- PTRH2 p.Leu17= Likely benign ★★ same type
- PTRH2 p.Val21Ile Benign/Likely benign ★★ same type
- PTRH2 p.Arg34Ter Likely pathogenic ★ same type
- PTRH2 p.Gln85Ter Likely pathogenic ★ same type
- PTRH2 p.Trp108Ter 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/ptrh2-p-ala56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown