CRTAM

protein-coding

cytotoxic and regulatory T cell molecule, the group of Nectins and nectin-like molecules|V-set domain containing|CD molecules|C2-set domain containing

Gene summary

The CRTAM gene is upregulated in CD4 (see MIM 186940)-positive and CD8 (see CD8A; MIM 186910)-positive T cells and encodes a type I transmembrane protein with V and C1-like Ig domains (Yeh et al., 2008 [PubMed 18329370]).[supplied by OMIM, Feb 2009]

MANE transcript

NM_019604.4

Inheritance

—

ClinVar variants

U:52B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr11:122,838,500-122,872,643

External References & Databases

Ensembl (ENSG00000109943)

Transcript & Mutation Effects

hg38 • Region Span ~34.1 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 CRTAM variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019604.4. 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			3 clinvar		2 clinvar	5
missense			48 clinvar	4 clinvar	4 clinvar	56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	52	4	6	62

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019604.4	RefSeq	NP_062550.2	10	MANE Select
ENST00000227348.9	Ensembl	ENSP00000227348.4	10	MANE Select
NM_001304782.2	RefSeq	NP_001291711.1	5	Standard
ENST00000533709.1	Ensembl	ENSP00000433728.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

T cell mediated cytotoxicity
detection of tumor cell
positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
cell recognition
positive regulation of natural killer cell mediated cytotoxicity

Molecular Function

signaling receptor binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000227348
Coding exons: 10
Length: 34140
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125746
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.372	189	204	0.927	0.0000101	2556
Missense (PolyPhen)		51	53.092	0.96059		696
Synonymous	0.00333	80	80.0	1.00	0.00000439	742
Loss of Function	1.00	15	19.8	0.757	9.30e-7	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00059	0.00059	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Interaction with CADM1 promotes natural killer (NK) cell cytotoxicity and interferon-gamma (IFN-gamma) secretion by CD8+ cells in vitro as well as NK cell-mediated rejection of tumors expressing CADM3 in vivo. {ECO:0000250|UniProtKB:Q149L7, ECO:0000269|PubMed:15811952}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.802
RVIS EVS: 0.6
RVIS percentile EVS: 82.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.210

Gene Damage Prediction

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