Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.2%, 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 -6 | GERP -4.5 |
| Overall | ||
| CADD | 1.013 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.2%
African / African-American · 7,666/75,018 alleles
Filtering AF
10%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.95%
Overall
0.577%
9,316/1,614,046 alleles · common
exomes 4,853/1,461,780 · genomes 4,463/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.2% | 10 |
| Middle Eastern | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.89% | 112 |
| Admixed American | 0.735% | 136 |
| European (non-Finnish) | 0.0468% | 2,138 |
| South Asian | 0.0274% | 3,643 |
| East Asian | 0.00669% | 14,959 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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.Phe78=
- Coding
- c.234C>T
- MANE Select
- NM_002840
- dbSNP
- rs6684279
- Type
- single nucleotide variant
- Location
- chr1:43553634 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.43 · 13 PDB
- Residue 78
- a β-strand; the ig-like c2-type 1 domain
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-phe78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown