PTPRF p.Phe1044=
c.3132T>C · rs781567773 · VCV3053366
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00254%, nfe)
Conditions
1
PTPRF-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.304 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 10.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00254%
European (non-Finnish) · 30/1,179,744 alleles
Filtering AF
0.0018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00157%
Overall
0.00198%
32/1,613,538 alleles · very rare
exomes 29/1,461,348 · genomes 3/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00254% | 39,325 |
| Admixed American | 0.00167% | 60,000 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
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.Phe1044=
- Coding
- c.3132T>C
- MANE Select
- NM_002840
- dbSNP
- rs781567773
- Type
- single nucleotide variant
- Location
- chr1:43604997 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.43 · 13 PDB
- Residue 1044
- the fibronectin type-iii 8 domain
Disease context
PTPRF-related disorder
Similar variants
- PTPRF c.3389+4T>G Likely benign same condition
- PTPRF c.3974-829C>T Likely benign same condition
- PTPRF c.4372-7C>T Likely benign same condition
- PTPRF p.Ala157= Benign same condition
- PTPRF p.Arg1286= Likely benign same condition
- PTPRF p.Asn441= Likely benign same condition
- PTPRF p.Asp562Asn Benign same condition
- PTPRF p.Asp650= Likely benign same condition
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-phe1044 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown