TRAT1

T cell receptor associated transmembrane adaptor 1

Basic information

Region (hg38): 3:108822770-108855005

Previous symbols: [ "TCRIM" ]

Links

ENSG00000163519 ∙ NCBI:50852 ∙ OMIM:604962 ∙ HGNC:30698 ∙ Uniprot:Q6PIZ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAT1 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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in TRAT1

This is a list of pathogenic ClinVar variants found in the TRAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-108838954-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-108849207-C-T			Benign (Mar 29, 2018)
3-108849234-G-C		not specified	Uncertain significance (Mar 13, 2023)
3-108849247-C-G		not specified	Uncertain significance (May 26, 2024)
3-108853647-G-A		not specified	Uncertain significance (May 02, 2024)
3-108853754-C-A		not specified	Uncertain significance (Oct 02, 2023)
3-108853755-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-108853773-G-A		not specified	Uncertain significance (Jul 14, 2022)
3-108853870-T-C		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAT1	protein_coding	protein_coding	ENST00000295756	6	32308

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0564	0.927	125556	0	182	125738	0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.361	112	102	1.10	0.00000501	1233
Missense in Polyphen		25	29.386	0.85074		399
Synonymous	-0.938	42	34.9	1.20	0.00000177	319
Loss of Function	2.09	4	11.7	0.342	6.81e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000612
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.0000544	0.0000544
South Asian	0.00405	0.00406
Other	0.000980	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stabilizes the TCR (T-cell antigen receptor)/CD3 complex at the surface of T-cells. {ECO:0000269|PubMed:11390434}.
• Pathway: Disease;Signal Transduction;Downstream TCR signaling;TCR signaling;TCR;Immune System;Adaptive Immune System;PIP3 activates AKT signaling;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Intracellular signaling by second messengers;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.587
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.327
• hipred: N
• hipred_score: 0.495
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trat1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of receptor recycling;adaptive immune response;cellular defense response;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;phosphatidylinositol phosphorylation;positive regulation of calcium-mediated signaling;T cell receptor signaling pathway;positive regulation of T cell receptor signaling pathway;negative regulation of transport;positive regulation of protein kinase B signaling
• Cellular component: plasma membrane;integral component of plasma membrane;T cell receptor complex
• Molecular function: transmembrane receptor protein tyrosine kinase adaptor activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity