Is PTPRC p.Phe1179= (c.3537T>C) pathogenic?

PTPRC p.Phe1179= (c.3537T>C) is classified Likely benign in PTPRC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-13). Very rare (popmax 0.00879%, sas); Associated with immunodeficiency 104.

What condition is associated with PTPRC p.Phe1179= (c.3537T>C)?

PTPRC p.Phe1179= (c.3537T>C) is associated with immunodeficiency 104 (ClinVar).

How common is PTPRC p.Phe1179= (c.3537T>C) in the general population?

PTPRC p.Phe1179= (c.3537T>C) is very rare (popmax 0.00879%, sas) (gnomAD).

PTPRC p.Phe1179=

c.3537T>C · rs191520732 · VCV800078

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00879%, sas)

Conditions

immunodeficiency 104

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.2	GERP -4.2
Overall
CADD	1.014	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00879% South Asian · 8/91,046 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00062% 10/1,611,618 alleles · very rare exomes 6/1,459,424 · genomes 4/152,194 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00879%	11,381
African / African-American	0.00267%	37,486

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.Phe1179=
Coding: c.3537T>C
MANE Select: NM_002838
dbSNP: rs191520732
Type: single nucleotide variant
Location: chr1:198754296 (GRCh38)
Gene constraint: LOEUF 0.343 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.22 · 6 PDB
Residue 1179: an α-helix; a UniProt-annotated variant site (in imd105); the tyrosine-protein phosphatase 2 domain

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 c.583+1G>A Likely pathogenic ★★ same condition
PTPRC c.583+1G>T Likely pathogenic ★★ same condition
PTPRC p.Arg890Ter Pathogenic/Likely pathogenic ★★ same condition
PTPRC c.1830-3C>T Uncertain significance ★★ same condition
PTPRC c.3509+5G>A Uncertain significance ★★ same condition
PTPRC p.Ala113Ser Uncertain significance ★★ ⚠ same condition
PTPRC p.Ala191Val Uncertain significance ★★ ⚠ same condition
PTPRC p.Ala60Thr Uncertain significance ★★ ⚠ 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-phe1179 (accessed [today's date]).

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