PTCRA

pre T cell antigen receptor alpha

Basic information

Region (hg38): 6:42915989-42925838

Links

ENSG00000171611 ∙ NCBI:171558 ∙ OMIM:606817 ∙ HGNC:21290 ∙ Uniprot:Q6ISU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 126	AR	Allergy/Immunology/Infectious; Endocrine	Individuals may have recurrent infections and other immunologic manifestations, and awareness may allow preventative measures, medical management (eg, with rituximab) as well as prompt and agressive treatment of infections; Hypothyroidism has been described, and awareness may allow medical management	Allergy/Immunology/Infectious; Endocrine	38422122

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCRA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCRA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			25	3	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	1

Variants in PTCRA

This is a list of pathogenic ClinVar variants found in the PTCRA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-42923035-G-A		not specified	Likely benign (Nov 28, 2023)
6-42923069-T-A		not specified	Uncertain significance (Jan 19, 2024)
6-42923071-C-G		not specified	Uncertain significance (Apr 26, 2024)
6-42923120-A-C		PTCRA POLYMORPHISM	Benign (Sep 04, 2024)
6-42923128-C-T		not specified	Uncertain significance (Nov 07, 2022)
6-42923145-C-G		not specified	Uncertain significance (Dec 20, 2021)
6-42923261-AGCTG-A		Immunodeficiency 126, susceptibility to	Pathogenic (Sep 04, 2024)
6-42923300-C-T		not specified	Uncertain significance (Dec 10, 2024)
6-42923316-C-G		not specified	Uncertain significance (Dec 16, 2022)
6-42923332-C-T		not specified	Uncertain significance (Aug 13, 2021)
6-42925264-CA-C		Immunodeficiency 126, susceptibility to	risk factor (Sep 04, 2024)
6-42925267-C-T		not specified	Uncertain significance (Dec 04, 2024)
6-42925282-G-A		Immunodeficiency 126, susceptibility to	risk factor (Sep 04, 2024)
6-42925296-C-T		not specified	Uncertain significance (Jun 10, 2024)
6-42925297-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-42925339-C-A		not specified	Uncertain significance (Jun 29, 2023)
6-42925339-C-T		not specified	Uncertain significance (May 18, 2022)
6-42925363-C-A		not specified	Uncertain significance (May 14, 2024)
6-42925369-C-G		not specified	Uncertain significance (Apr 27, 2022)
6-42925369-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-42925378-C-G		not specified	Uncertain significance (Jul 14, 2021)
6-42925395-C-T		not specified	Uncertain significance (Sep 04, 2024)
6-42925410-G-A		not specified	Uncertain significance (Aug 12, 2024)
6-42925429-C-T		not specified	Likely benign (Nov 26, 2024)
6-42925443-G-C		not specified	Uncertain significance (Nov 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCRA	protein_coding	protein_coding	ENST00000304672	4	9847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.144	0.786	125667	0	31	125698	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0963	157	160	0.979	0.00000888	1720
Missense in Polyphen		45	45.462	0.98984		577
Synonymous	0.901	63	72.8	0.866	0.00000419	669
Loss of Function	1.47	2	5.84	0.342	2.52e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000901	0.000901
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The pre-T-cell receptor complex (composed of PTCRA, TCRB and the CD3 complex) regulates early T-cell development. {ECO:0000250}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Notch Signaling Pathway;Notch Signaling Pathway;Notch Signaling Pathway;Signal Transduction;NOTCH3 Intracellular Domain Regulates Transcription;Signaling by NOTCH3;Signaling by NOTCH;C-MYB transcription factor network;Notch signaling pathway (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.624
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.8

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.123
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000672

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptcra
• Phenotype: hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of thymocyte apoptotic process
• Cellular component: integral component of membrane
• Molecular function: protein binding