PTPRG p.Ser433=
c.1299C>T · rs763904315 · VCV760879
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, 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 -6.9 | GERP -4.6 |
| Overall | ||
| CADD | 3.232 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,946 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00198%
32/1,614,110 alleles · ultra-rare
exomes 22/1,461,892 · genomes 10/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,747 |
| Admixed American | 0.005% | 20,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| European (non-Finnish) | 0.000593% | 168,580 |
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.Ser433=
- Coding
- c.1299C>T
- MANE Select
- NM_002841
- dbSNP
- rs763904315
- Type
- single nucleotide variant
- Location
- chr3:62195142 (GRCh38)
- Gene constraint
- LOEUF 0.714 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.76 · 20 PDB
- Residue 433
- the fibronectin type-iii domain
Similar variants
- 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.Pro58= 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-ser433 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown