PTCRA

Chr 6AR

pre T cell antigen receptor alpha

Also known as: IMD126, PT-ALPHA, PTA

NCBI Gene: 171558ENSG00000171611UniProt: Q6ISU1

The protein encoded by this gene is a single-pass type I membrane protein that is found in immmature but not mature T-cells. Along with TCRB and CD3 complex, the encoded protein forms the pre-T-cell receptor complex, which regulates early T-cell development. Four transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]

Primary Disease Associations & Inheritance

Immunodeficiency 126MIM #620931
AR
61
ClinVar variants
9
Pathogenic / LP
0.14
pLI score
0
Active trials
Clinical Summary— PTCRA
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.34) despite low pLI — interpret in context.
📋
ClinVar Variants
9 Pathogenic / Likely Pathogenic· 45 VUS of 61 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.07LOEUF
pLI 0.144
Z-score 1.47
OE 0.34 (0.14–1.07)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.10Z-score
OE missense 0.98 (0.86–1.12)
157 obs / 160.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.34 (0.14–1.07)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.98 (0.86–1.12)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.87
0≤1.21.6
LoF obs/exp: 2 / 5.8Missense obs/exp: 157 / 160.4Syn Z: 0.90

ClinVar Variant Classifications

61 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9
VUS45
Likely Benign6
Benign1
9
Pathogenic
45
VUS
6
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
8
0
9
Likely Pathogenic
0
0
0
0
0
VUS
0
40
5
0
45
Likely Benign
0
6
0
0
6
Benign
0
1
0
0
1
Total14713061

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PTCRA · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Immunodeficiency 126

MIM #620931

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Rheumatoid arthritis, systemic lupus erythematosus and primary Sjögren's syndrome shared megakaryocyte expansion in peripheral blood.
Wang Y et al.·Ann Rheum Dis
2022
The immunopathological landscape of human pre-TCRα deficiency: From rare to common variants.
Materna M et al.·Science
2024
Clinical outcome of percutaneous transluminal coronary rotational atherectomy in patients with end-stage renal disease.
Aoki J et al.·Circ J
2003Cohort
Prognostic gene landscapes and therapeutic insights in sepsis-induced coagulopathy.
Ran X et al.·Thromb Res
2024
Predictors of Recurrent In-Stent Restenosis After Paclitaxel-Coated Balloon Angioplasty.
Koiwaya H et al.·Circ J
2017Clinical trial
Differences in symptoms during and post PTCA versus rotational ablation.
Murphy MC et al.·Prog Cardiovasc Nurs
1994
Evidence for a stepwise program of extrathymic T cell development within the human tonsil.
McClory S et al.·J Clin Invest
2012
An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma.
Tang G et al.·BMC Bioinformatics
2023
Expression of T-lineage-affiliated transcripts and TCR rearrangements in acute promyelocytic leukemia: implications for the cellular target of t(15;17).
Chapiro E et al.·Blood
2006
Human skin-derived keratinocytes and fibroblasts co-cultured on 3D poly ε-caprolactone scaffold support in vitro HSC differentiation into T-lineage committed cells.
Palamaro L et al.·Int Immunol
2013
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools