PTPRF p.Pro708=
c.2124C>T · rs147762557 · VCV732353
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.331%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.523 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.38 | GERP -4.5, phastCons 0.99 |
| Overall | ||
| CADD | 8.205 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.331%
Middle Eastern · 20/6,048 alleles
Filtering AF
0.219%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.183%
Overall
0.123%
1,988/1,612,902 alleles · rare
exomes 1,868/1,460,546 · genomes 120/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.331% | 302 |
| European (non-Finnish) | 0.146% | 686 |
| Remaining individualsnot grpmax-eligible | 0.104% | 961 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0948% | 1,055 |
| South Asian | 0.0835% | 1,197 |
| Admixed American | 0.0634% | 1,578 |
| African / African-American | 0.032% | 3,127 |
| Finnishnot grpmax-eligible | 0.0281% | 3,555 |
| East Asian | 0.00223% | 44,852 |
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
- PTPRF
- Protein
- p.Pro708=
- Coding
- c.2124C>T
- MANE Select
- NM_002840
- dbSNP
- rs147762557
- Type
- single nucleotide variant
- Location
- chr1:43598724 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.43 · 13 PDB
- Residue 708
- the 'disordered' region
Similar variants
- PTPRF p.Gly1143Ser Uncertain significance ★★ ⚠ same type
- PTPRF p.His1730Gln Uncertain significance ★★ ⚠ same type
- PTPRF c.1531+9G>A Benign/Likely benign ★★ same type
- PTPRF c.1668+10G>C Benign/Likely benign ★★ same type
- PTPRF c.237+5G>A Benign ★★ same type
- PTPRF c.3974-9C>T Benign ★★ same type
- PTPRF p.Ala1659= Benign ★★ same type
- PTPRF p.Ala356Ser Likely benign ★★ 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/ptprf-p-pro708 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown