TRAT1

protein-coding

T cell receptor associated transmembrane adaptor 1

Gene summary

Predicted to enable transmembrane receptor protein tyrosine kinase adaptor activity. Acts upstream of or within negative regulation of receptor recycling; negative regulation of transport; and positive regulation of signal transduction. Located in centriolar satellite and plasma membrane. Part of T cell receptor complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

TCRIM

MANE transcript

NM_016388.4

Inheritance

—

ClinVar variants

U:27B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr3:108,822,770-108,855,005

External References & Databases

Ensembl (ENSG00000163519)

Transcript & Mutation Effects

hg38 • Region Span ~32.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRAT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016388.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			27 clinvar	3 clinvar	1 clinvar	31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	3	1	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016388.4	RefSeq	NP_057472.2	6	MANE Select
ENST00000295756.11	Ensembl	ENSP00000295756.6	6	MANE Select
NM_001317747.2	RefSeq	NP_001304676.1	5	Standard
ENST00000426646.1	Ensembl	ENSP00000410097.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Disease
Signal Transduction
Downstream TCR signaling
TCR signaling
TCR

Biological Process

negative regulation of receptor recycling
adaptive immune response
cellular defense response
signal transduction
transmembrane receptor protein tyrosine kinase signaling pathway

Molecular Function

transmembrane receptor protein tyrosine kinase adaptor activity
phosphatidylinositol-4,5-bisphosphate 3-kinase activity

Cellular Component

plasma membrane
integral component of plasma membrane
T cell receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295756
Coding exons: 6
Length: 32308
Individuals with no LoFs: 125556
Homozygous LoFs: 0
Heterozygous LoFs: 182
Defined: 125738
p: 0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.361	112	102	1.10	0.00000501	1233
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.0041	0.0041	notable
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Stabilizes the TCR (T-cell antigen receptor)/CD3 complex at the surface of T-cells. {ECO:0000269|PubMed:11390434}.;

Recessive Scores

pRec: 0.228

Intolerance Scores

LoFtool: 0.587
RVIS EVS: 0.53
RVIS percentile EVS: 80.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.963

Gene Damage Prediction

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