PTRH2 p.Ser62=
c.186C>T · rs1037221821 · VCV3043794
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
PTRH2-related disorder
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 2.3 | GERP -0.67, phastCons 0.99 |
| Overall | ||
| CADD | 8.975 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,994 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.000805%
13/1,613,964 alleles · very rare
exomes 9/1,461,886 · genomes 4/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,994 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00134% | 74,872 |
| European (non-Finnish) | 0.000847% | 118,002 |
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.Ser62=
- Coding
- c.186C>T
- MANE Select
- NM_016077
- dbSNP
- rs1037221821
- Type
- single nucleotide variant
- Location
- chr17:59697793 (GRCh38)
- Gene constraint
- LOEUF 1.322 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 1 PDB
Disease context
PTRH2-related disorder
Similar variants
- PTRH2 p.Gln85Pro Pathogenic ★★ same type
- PTRH2 c.1-124A>G Likely benign ★★ same type
- PTRH2 p.Ala56= Benign/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-ser62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown