PTPRF p.Ala1607=
c.4821T>C · rs145219690 · VCV752442
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.281%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.173 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -4.5 |
| Overall | ||
| CADD | 4.361 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.281%
African / African-American · 211/75,068 alleles
Filtering AF
0.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.238%
Overall
0.0139%
225/1,614,074 alleles · rare
exomes 94/1,461,720 · genomes 131/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.281% | 356 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| Admixed American | 0.00833% | 12,006 |
| South Asian | 0.0011% | 91,088 |
| European (non-Finnish) | 8.47e-05% | 1,180,038 |
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.Ala1607=
- Coding
- c.4821T>C
- MANE Select
- NM_002840
- dbSNP
- rs145219690
- Type
- single nucleotide variant
- Location
- chr1:43619462 (GRCh38)
- Gene constraint
- LOEUF 0.348 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.43 · 13 PDB
- Residue 1607
- an α-helix; the tyrosine-protein phosphatase 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-ala1607 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown