Is PTPRF p.Asp650= (c.1950C>T) pathogenic?

PTPRF p.Asp650= (c.1950C>T) is classified Likely benign in PTPRF (ClinVar, No assertion criteria, 1 submitter). Ultra-rare (popmax 0.0169%, amr); Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with PTPRF p.Asp650= (c.1950C>T)?

PTPRF p.Asp650= (c.1950C>T) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is PTPRF p.Asp650= (c.1950C>T) in the general population?

PTPRF p.Asp650= (c.1950C>T) is ultra-rare (popmax 0.0169%, amr) (gnomAD).

PTPRF p.Asp650=

c.1950C>T · rs774549273 · VCV2681506

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0169%, amr)

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.059	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.48	GERP -2.3, phastCons 1
Overall
CADD	14.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0169% Admixed American · 10/59,256 alleles

Filtering AF 0.0091% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00689%

Overall 0.00199% 32/1,607,682 alleles · ultra-rare exomes 30/1,455,458 · genomes 2/152,224 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0169%	5,926
South Asian	0.00224%	44,672
Remaining individualsnot grpmax-eligible	0.00161%	62,214
European (non-Finnish)	0.00153%	65,424
African / African-American	0.00134%	74,884

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.Asp650=
Coding: c.1950C>T
MANE Select: NM_002840
dbSNP: rs774549273
Type: single nucleotide variant
Location: chr1:43597884 (GRCh38)
Gene constraint: LOEUF 0.348 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.43 · 13 PDB
Residue 650: a β-strand; the fibronectin type-iii 4 domain

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

Disease context

EBV-positive nodal T- and NK-cell lymphoma

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.Ile1819= 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-asp650 (accessed [today's date]).

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