PTPRG p.Pro58=
c.174G>A · rs77715924 · VCV775881
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.18%, afr) — too common for a highly-penetrant pathogenic allele
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 -7.8 | GERP -4.4 |
| Overall | ||
| CADD | 3.267 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.18%
African / African-American · 4,634/74,936 alleles
Filtering AF
6.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.97%
Overall
0.32%
5,159/1,611,482 alleles · common
exomes 2,482/1,459,340 · genomes 2,677/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.18% | 16 |
| Remaining individualsnot grpmax-eligible | 0.407% | 246 |
| Admixed American | 0.331% | 302 |
| Middle Eastern | 0.149% | 671 |
| South Asian | 0.021% | 4,767 |
| East Asian | 0.00669% | 14,947 |
| European (non-Finnish) | 0.00356% | 28,067 |
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
- PTPRG
- Protein
- p.Pro58=
- Coding
- c.174G>A
- MANE Select
- NM_002841
- dbSNP
- rs77715924
- Type
- single nucleotide variant
- Location
- chr3:61748966 (GRCh38)
- Gene constraint
- LOEUF 0.714 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.76 · 20 PDB
- Residue 58
- the alpha-carbonic anhydrase domain
Similar variants
- PTPRG p.Pro58Ser Uncertain significance ★ ⚠ same residue
- PTPRG p.Ala614Thr Uncertain significance ★★ ⚠ same type
- PTPRG p.Ile1333Thr Uncertain significance ★★ ⚠ same type
- PTPRG p.Asn429= Likely benign ★★ same type
- PTPRG p.His412= Benign ★★ same type
- PTPRG p.Leu14= Benign ★★ same type
- PTPRG p.Ala1062Thr Uncertain significance ★ ⚠ same type
- PTPRG p.Ala1190Thr Uncertain significance ★ ⚠ 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/ptprg-p-pro58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown