Is PTPRF p.Pro609= (c.1827T>A) pathogenic?

PTPRF p.Pro609= (c.1827T>A) is classified Likely benign in PTPRF (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.363%, eas).

How common is PTPRF p.Pro609= (c.1827T>A) in the general population?

PTPRF p.Pro609= (c.1827T>A) is rare (popmax 0.363%, eas) (gnomAD).

PTPRF p.Pro609=

c.1827T>A · rs751860015 · VCV747245

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.363%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.144	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP -2, phastCons 1
Overall
CADD	13.64	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.363% East Asian · 68/18,708 alleles

Filtering AF 0.345% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.34%

Overall 0.309% 2,417/782,686 alleles · rare exomes 2,408/685,118 · genomes 9/97,568 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.409%	245
East Asiangrpmax	0.363%	275
European (non-Finnish)	0.358%	279
Ashkenazi Jewishnot grpmax-eligible	0.267%	374
Middle Eastern	0.173%	578
African / African-American	0.158%	632
Admixed American	0.111%	903
Finnishnot grpmax-eligible	0.0884%	1,131
South Asian	0.08%	1,250

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro609=
Coding: c.1827T>A
MANE Select: NM_002840
dbSNP: rs751860015
Type: single nucleotide variant
Location: chr1:43597761 (GRCh38)
Gene constraint: LOEUF 0.348 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.43 · 13 PDB
Residue 609: the fibronectin type-iii 4 domain

Full PTPRF gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-pro609 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown