CRTAM

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

Basic information

Region (hg38): 11:122838500-122872643

Links

ENSG00000109943 ∙ NCBI:56253 ∙ OMIM:612597 ∙ HGNC:24313 ∙ Uniprot:O95727 ∙ 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 CRTAM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRTAM 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					2	2
missense			13	1	4	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	6

Variants in CRTAM

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

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

Position	Type	Phenotype	Significance	ClinVar
11-122838555-G-T		not specified	Uncertain significance (Feb 28, 2024)
11-122838560-T-A		not specified	Uncertain significance (Jan 08, 2024)
11-122850068-A-C			Benign (Jun 29, 2018)
11-122850119-C-T		not specified	Uncertain significance (May 28, 2024)
11-122850207-G-C		not specified	Uncertain significance (Jan 24, 2024)
11-122851732-C-A			Benign (Jun 29, 2018)
11-122851791-T-G		not specified	Uncertain significance (Apr 23, 2024)
11-122851806-G-A		not specified	Likely benign (Nov 13, 2023)
11-122854037-G-A			Benign (Jun 21, 2018)
11-122855722-A-G			Benign (May 08, 2018)
11-122855746-G-A		not specified	Uncertain significance (Jun 05, 2023)
11-122855747-C-A		not specified	Uncertain significance (Jun 17, 2024)
11-122855782-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-122855783-G-A			Benign (Jun 29, 2018)
11-122864636-T-C		not specified	Uncertain significance (Jan 20, 2023)
11-122864660-C-T			Benign (May 08, 2018)
11-122864677-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-122867415-A-G		not specified	Uncertain significance (Jan 27, 2022)
11-122867421-A-G		not specified	Uncertain significance (Sep 26, 2022)
11-122867517-T-C		not specified	Uncertain significance (Dec 07, 2021)
11-122868018-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-122871296-A-G		not specified	Uncertain significance (Jan 18, 2023)
11-122871343-G-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRTAM	protein_coding	protein_coding	ENST00000227348	10	34140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.06e-9	0.480	125699	0	47	125746	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	189	204	0.927	0.0000101	2556
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000591	0.000588
Other	0.000498	0.000489

dbNSFP

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}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.78

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.146
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crtam
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• 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;positive regulation of cytokine secretion;regulation of immune response;activated T cell proliferation;detection of stimulus
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding