Is PTPRC p.Pro44= (c.132A>G) pathogenic?

PTPRC p.Pro44= (c.132A>G) is classified Benign/Likely benign in PTPRC (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-05-01). Low-frequency (popmax 1.04%, afr); Associated with immunodeficiency 104.

What condition is associated with PTPRC p.Pro44= (c.132A>G)?

PTPRC p.Pro44= (c.132A>G) is associated with immunodeficiency 104 (ClinVar).

How common is PTPRC p.Pro44= (c.132A>G) in the general population?

PTPRC p.Pro44= (c.132A>G) is low-frequency (popmax 1.04%, afr) (gnomAD).

PTPRC p.Pro44=

c.132A>G · rs115797104 · VCV391024

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.04%, afr)

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 0.86	GERP -0.037
Overall
CADD	2.052	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.04% African / African-American · 777/74,998 alleles

Filtering AF 0.976% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.952%

Overall 0.0527% 850/1,614,062 alleles · low-frequency exomes 399/1,461,820 · genomes 451/152,242 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.04%	97
Admixed American	0.0616%	1,622
Remaining individualsnot grpmax-eligible	0.0512%	1,953
Middle Eastern	0.0165%	6,060
South Asian	0.0011%	91,086
European (non-Finnish)	0.000169%	589,984

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.Pro44=
Coding: c.132A>G
MANE Select: NM_002838
dbSNP: rs115797104
Type: single nucleotide variant
Location: chr1:198696743 (GRCh38)
Gene constraint: LOEUF 0.343 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.22 · 6 PDB
Residue 44: 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 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-pro44 (accessed [today's date]).

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