CD2

CD2 molecule, the group of V-set domain containing|CD molecules|C2-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 1:116754429-116769229

Previous symbols: [ "SRBC" ]

Links

ENSG00000116824 ∙ NCBI:914 ∙ OMIM:186990 ∙ HGNC:1639 ∙ Uniprot:P06729 ∙ 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 CD2 gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD2 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					1	1
missense			15	3		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	15	3	1

Variants in CD2

This is a list of pathogenic ClinVar variants found in the CD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-116754643-A-G		not specified	Uncertain significance (Aug 28, 2023)
1-116754652-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-116754682-G-A		not specified	Likely benign (Jul 29, 2023)
1-116754690-A-C		not specified	Uncertain significance (May 31, 2023)
1-116754708-A-G		not specified	Likely benign (Dec 17, 2023)
1-116754715-A-G		not specified	Uncertain significance (Oct 18, 2021)
1-116754808-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-116754831-A-C		not specified	Uncertain significance (Jul 12, 2022)
1-116754851-T-G		not specified	Uncertain significance (Jul 20, 2021)
1-116754852-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-116754875-G-T		not specified	Uncertain significance (Nov 23, 2022)
1-116760438-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-116764484-A-G		Inborn genetic diseases	Uncertain significance (Nov 10, 2021)
1-116764502-A-C		not specified	Uncertain significance (Jun 30, 2023)
1-116764516-A-G		not specified	Uncertain significance (Apr 04, 2023)
1-116764539-G-C		not specified	Likely benign (Feb 22, 2023)
1-116764561-G-A		not specified	Likely benign (Jun 01, 2023)
1-116768535-G-A		not specified	Uncertain significance (Jul 14, 2023)
1-116768613-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-116768672-G-A			Benign (Apr 23, 2018)
1-116768701-G-C		Malignant tumor of prostate	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD2	protein_coding	protein_coding	ENST00000369478	5	14844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.471	0.524	125538	0	1	125539	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0669	191	194	0.986	0.00000993	2312
Missense in Polyphen		37	52.759	0.7013		648
Synonymous	-0.720	79	71.3	1.11	0.00000380	678
Loss of Function	2.36	2	10.1	0.198	4.20e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: CD2 interacts with lymphocyte function-associated antigen CD58 (LFA-3) and CD48/BCM1 to mediate adhesion between T- cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);stathmin and breast cancer resistance to antimicrotubule agents;ras-independent pathway in nk cell-mediated cytotoxicity;TCR;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.265

Intolerance Scores

• loftool: 0.142
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Haploinsufficiency Scores

• pHI: 0.300
• hipred: Y
• hipred_score: 0.504
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd2
• Phenotype: normal phenotype

Gene ontology

• Biological process: membrane raft polarization;apoptotic process;cell surface receptor signaling pathway;natural killer cell activation;positive regulation of myeloid dendritic cell activation;positive regulation of tumor necrosis factor production;heterotypic cell-cell adhesion;T cell activation;regulation of T cell differentiation;leukocyte migration;cell-cell adhesion;positive regulation of interferon-gamma secretion;positive regulation of interleukin-8 secretion
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface
• Molecular function: signaling receptor binding;protein binding;signaling receptor activity