Is PTPRC p.Pro87fs (c.260del) pathogenic?

PTPRC p.Pro87fs (c.260del) is classified Pathogenic in PTPRC (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-12). Very rare (popmax 0.000169%, nfe); Associated with immunodeficiency 104.

What condition is associated with PTPRC p.Pro87fs (c.260del)?

PTPRC p.Pro87fs (c.260del) is associated with immunodeficiency 104 (ClinVar).

How common is PTPRC p.Pro87fs (c.260del) in the general population?

PTPRC p.Pro87fs (c.260del) is very rare (popmax 0.000169%, nfe) (gnomAD).

PTPRC p.Pro87fs

c.260del · rs1666230230 · VCV2868091

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Conditions

immunodeficiency 104

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.7	GERP -3.4
Overall
CADD	18.05	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000169% European (non-Finnish) · 2/1,179,986 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,613,972 alleles · very rare exomes 1/1,461,824 · genomes 1/152,148 · joint denominator

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: PTPRC
Protein: p.Pro87fs
Coding: c.260del
MANE Select: NM_002838
dbSNP: rs1666230230
Type: Deletion
Location: chr1:198696868 (GRCh38)
Gene constraint: LOEUF 0.343 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.22 · 6 PDB
Residue 87: the 'disordered' region

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

Disease context

immunodeficiency 104 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTPRC p.Pro87= Likely benign ★★ same residue
PTPRC p.Pro87Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
PTPRC c.1864+4_1864+7del Uncertain significance ★★ same condition
PTPRC c.2561+27del Benign/Likely benign ★★ same condition
PTPRC c.2848-4del Benign/Likely benign ★★ same condition
PTPRC c.2848-5_2848-4del Benign/Likely benign ★★ same condition
PTPRC c.659-12del Benign/Likely benign ★★ same condition
PTPRC p.Glu874fs Pathogenic ★ 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/ptprc-p-pro87fs (accessed [today's date]).

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