Is PTPRF p.Pro536Ala (c.1606C>G) pathogenic?

PTPRF p.Pro536Ala (c.1606C>G) is classified Uncertain significance in PTPRF (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-26). AlphaMissense: likely benign (0.0944); Ultra-rare (popmax 0.0887%, nfe).

How common is PTPRF p.Pro536Ala (c.1606C>G) in the general population?

PTPRF p.Pro536Ala (c.1606C>G) is ultra-rare (popmax 0.0887%, nfe) (gnomAD).

What do computational predictors say about PTPRF p.Pro536Ala (c.1606C>G)?

AlphaMissense predicts likely benign (score 0.0944) — an in-silico prediction, not a clinical call.

PTPRF p.Pro536Ala

c.1606C>G · rs139284587 · VCV2272172

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0944 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0887%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.0944	likely benign
REVEL	0.369	indeterminate
SaProt	LLR -5.56	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 2.1, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 6,728 bp · p 0.011 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0887% European (non-Finnish) · 1,047/1,180,016 alleles

Filtering AF 0.0842% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0824%

Overall 0.0683% 1,102/1,613,466 alleles · ultra-rare exomes 1,034/1,461,188 · genomes 68/152,278 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0887%	1,127
Remaining individualsnot grpmax-eligible	0.0368%	2,717
South Asian	0.0165%	6,072
African / African-American	0.0147%	6,821
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,802
Admixed American	0.005%	20,008
East Asian	0.00223%	44,878

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.Pro536Ala
Coding: c.1606C>G
MANE Select: NM_002840
dbSNP: rs139284587
Type: single nucleotide variant
Location: chr1:43591886 (GRCh38)
Gene constraint: LOEUF 0.348 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.43 · 13 PDB
Residue 536: the fibronectin type-iii 3 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-pro536ala (accessed [today's date]).

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