CD2

protein-coding

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

Gene summary

The protein encoded by this gene is a surface antigen found on all peripheral blood T-cells. The encoded protein interacts with LFA3 (CD58) on antigen presenting cells to optimize immune recognition. A locus control region (LCR) has been found in the 3' flanking sequence of this gene. [provided by RefSeq, Jun 2016]

Previous symbols:

SRBC

MANE transcript

NM_001767.5

Inheritance

—

ClinVar variants

U:57B:9

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr1:116,754,430-116,769,229

External References & Databases

Ensembl (ENSG00000116824)

Transcript & Mutation Effects

hg38 • Region Span ~14.8 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 CD2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001767.5. 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					1 clinvar	1
missense			57 clinvar	8 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	8	1	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001767.5	RefSeq	NP_001758.2	5	MANE Select
ENST00000369478.4	Ensembl	ENSP00000358490.3	5	MANE Select
NM_001328609.2	RefSeq	NP_001315538.1	5	Standard
ENST00000369477.1	Ensembl	ENSP00000358489.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

membrane raft polarization
apoptotic process
cell surface receptor signaling pathway
natural killer cell activation
positive regulation of myeloid dendritic cell activation

Molecular Function

signaling receptor binding
protein binding
signaling receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
external side of plasma membrane
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369478
Coding exons: 5
Length: 14844
Individuals with no LoFs: 125538
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125539
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0669	191	194	0.986	0.00000993	2312
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.265

Intolerance Scores

LoFtool: 0.142
RVIS EVS: 0.4
RVIS percentile EVS: 76.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.815

Gene Damage Prediction

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