CD48

Summary

CD48 (CD48 molecule, HGNC:1683) is a protein-coding gene on chromosome 1q23.3, encoding CD48 antigen (P09326). Glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein that interacts via its N-terminal immunoglobulin domain with cell surface receptors including CD244/2B4 or CD2 to regulate immune cell function and activation.

This gene encodes a member of the CD2 subfamily of immunoglobulin-like receptors which includes SLAM (signaling lymphocyte activation molecules) proteins. The encoded protein is found on the surface of lymphocytes and other immune cells, dendritic cells and endothelial cells, and participates in activation and differentiation pathways in these cells. The encoded protein does not have a transmembrane domain, however, but is held at the cell surface by a GPI anchor via a C-terminal domain which maybe cleaved to yield a soluble form of the receptor. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 962 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 55 total
• GTEx eGene: eQTL in 7 tissues, sQTL in 5 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.31 (unconstrained)
• MANE Select transcript: NM_001778
• Interaction hub: 2,226 STRING partners (top 6% of genes corpus-wide)
• Notable: 55 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1683
Approved symbol	CD48
Name	CD48 molecule
Location	1q23.3
Locus type	gene with protein product
Status	Approved
Aliases	BLAST, mCD48, hCD48, SLAMF2
Ensembl gene	ENSG00000117091
Ensembl biotype	protein_coding
OMIM	109530
Entrez	962

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 3 nonsense_mediated_decay

MANE Select: ENST00000368046

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3

ENST00000368046, ENST00000368045, ENST00000613788, ENST00000902592, ENST00000902593, ENST00001104357, ENST00001104358, ENST00001104359, ENST00001104360, ENST00001104361, ENST00001116597, ENST00001143569

RefSeq mRNA: 2 — MANE Select: NM_001778 NM_001256030, NM_001778

CCDS: CCDS1208, CCDS72955

Canonical transcript exons

ENST00000368046 — 4 exons

Exon	Start	End
ENSE00001166175	160681202	160681468
ENSE00001166183	160684887	160685189
ENSE00001446197	160678746	160679131
ENSE00001920767	160711682	160711822

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 99.52.

FANTOM5 (CAGE): breadth broad, TPM avg 68.3544 / max 2199.8164, expressed in 460 samples.

Highest expression (Bgee): monocyte, leukocyte, mononuclear cell, granulocyte, blood.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CD48 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 7 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

12 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Whole Blood	sqtl	4.7e-141	+1.50	1:160684968:C:G
Spleen	sqtl	6.9e-59	+1.77	1:160684968:C:G
Whole Blood	eqtl	6.7e-08	-0.15	1:160704478:A:C
Cells EBV-transformed lymphocytes	eqtl	2.8e-05	+0.15	1:160711985:A:G
Cells EBV-transformed lymphocytes	sqtl	8.2e-05	-0.48	1:160684968:C:G
Adipose Subcutaneous	sqtl	3.9e-03	-1.05	1:160153986:C:G
Nerve Tibial	eqtl	9.5e-03	+0.23	1:160182592:C:T
Skin Sun Exposed Lower leg	eqtl	9.5e-03	+0.14	1:160689370:G:A
Ovary	eqtl	1.9e-02	+0.44	1:160172204:C:T
Small Intestine Terminal Ileum	sqtl	2.4e-02	+1.11	1:160684968:C:G
Stomach	eqtl	3.8e-02	+0.51	1:161154267:G:T
Esophagus Muscularis	eqtl	4.6e-02	-0.22	1:161086424:G:C

FANTOM5 promoters

4 alternative TSS:

Promoter ID	TPM avg	Samples expressed
15527	57.0048	447
15526	11.1720	335
15528	0.1292	81
15529	0.0484	32

Top tissues by expression

showing 100 of 281 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	99.52	gold quality
leukocyte	CL:0000738	99.52	gold quality
mononuclear cell	CL:0000842	99.52	gold quality
granulocyte	CL:0000094	99.48	gold quality
blood	UBERON:0000178	98.19	gold quality
bone marrow cell	CL:0002092	98.06	gold quality
vermiform appendix	UBERON:0001154	97.83	gold quality
spleen	UBERON:0002106	97.83	gold quality
lymph node	UBERON:0000029	97.40	gold quality
bone marrow	UBERON:0002371	97.39	gold quality
caecum	UBERON:0001153	94.54	gold quality
colonic epithelium	UBERON:0000397	93.82	gold quality
epithelium of nasopharynx	UBERON:0001951	92.38	gold quality
rectum	UBERON:0001052	92.37	gold quality
trabecular bone tissue	UBERON:0002483	92.27	gold quality
gall bladder	UBERON:0002110	91.59	gold quality
periodontal ligament	UBERON:0008266	90.15	gold quality
thymus	UBERON:0002370	88.97	gold quality
tonsil	UBERON:0002372	87.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.56	gold quality
superficial temporal artery	UBERON:0001614	87.11	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.89	gold quality
mucosa of transverse colon	UBERON:0004991	86.41	gold quality
small intestine	UBERON:0002108	85.46	gold quality
upper lobe of left lung	UBERON:0008952	84.89	gold quality
decidua	UBERON:0002450	84.14	silver quality
upper lobe of lung	UBERON:0008948	83.81	gold quality
duodenum	UBERON:0002114	83.01	gold quality
right lung	UBERON:0002167	82.61	gold quality
jejunal mucosa	UBERON:0000399	82.44	gold quality
lung	UBERON:0002048	81.81	gold quality
mucosa of urinary bladder	UBERON:0001259	81.33	silver quality
mucosa of sigmoid colon	UBERON:0004993	81.20	gold quality
right coronary artery	UBERON:0001625	80.81	gold quality
colonic mucosa	UBERON:0000317	80.36	gold quality
ileal mucosa	UBERON:0000331	79.61	silver quality
omental fat pad	UBERON:0010414	79.60	gold quality
peritoneum	UBERON:0002358	79.55	gold quality
adipose tissue of abdominal region	UBERON:0007808	79.34	gold quality
intestine	UBERON:0000160	78.49	gold quality
transverse colon	UBERON:0001157	78.32	gold quality
palpebral conjunctiva	UBERON:0001812	77.90	gold quality
smooth muscle tissue	UBERON:0001135	77.13	gold quality
buccal mucosa cell	CL:0002336	76.72	silver quality
urinary bladder	UBERON:0001255	76.47	gold quality
large intestine	UBERON:0000059	76.45	gold quality
pylorus	UBERON:0001166	75.97	gold quality
oral cavity	UBERON:0000167	75.94	gold quality
colon	UBERON:0001155	75.86	gold quality
right lobe of liver	UBERON:0001114	75.52	gold quality
jejunum	UBERON:0002115	75.20	gold quality
skin of hip	UBERON:0001554	74.97	gold quality
calcaneal tendon	UBERON:0003701	74.94	gold quality
nasal cavity epithelium	UBERON:0005384	74.70	gold quality
amniotic fluid	UBERON:0000173	74.66	gold quality
body of stomach	UBERON:0001161	74.65	gold quality
lower lobe of lung	UBERON:0008949	74.60	silver quality
adipose tissue	UBERON:0001013	74.49	gold quality
liver	UBERON:0002107	74.38	gold quality
connective tissue	UBERON:0002384	74.19	gold quality
stomach	UBERON:0000945	74.01	gold quality
nasal cavity mucosa	UBERON:0001826	73.92	gold quality
fundus of stomach	UBERON:0001160	73.60	gold quality
minor salivary gland	UBERON:0001830	73.48	gold quality
epithelial cell of pancreas	CL:0000083	73.39	gold quality
cardia of stomach	UBERON:0001162	73.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.97	gold quality
subcutaneous adipose tissue	UBERON:0002190	72.86	gold quality
saliva-secreting gland	UBERON:0001044	72.74	gold quality
mammary duct	UBERON:0001765	72.74	silver quality
adult organism	UBERON:0007023	72.57	silver quality
pleura	UBERON:0000977	72.54	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.54	gold quality
germinal epithelium of ovary	UBERON:0001304	72.50	silver quality
left uterine tube	UBERON:0001303	72.44	gold quality
descending thoracic aorta	UBERON:0002345	72.29	gold quality
coronary artery	UBERON:0001621	72.26	gold quality
superior surface of tongue	UBERON:0007371	72.08	gold quality
left coronary artery	UBERON:0001626	72.00	gold quality
parietal pleura	UBERON:0002400	71.99	gold quality
mouth mucosa	UBERON:0003729	71.89	gold quality
uterine cervix	UBERON:0000002	71.73	gold quality
esophagus mucosa	UBERON:0002469	71.41	gold quality
trachea	UBERON:0003126	71.36	silver quality
spinal cord	UBERON:0002240	71.24	gold quality
thoracic aorta	UBERON:0001515	71.17	gold quality
ascending aorta	UBERON:0001496	71.15	gold quality
vagina	UBERON:0000996	71.12	gold quality
prostate gland	UBERON:0002367	70.91	gold quality
right uterine tube	UBERON:0001302	70.80	gold quality
myocardium	UBERON:0002349	70.68	gold quality
visceral pleura	UBERON:0002401	70.65	gold quality
thoracic mammary gland	UBERON:0005200	70.44	gold quality
fallopian tube	UBERON:0003889	70.33	gold quality
mammary gland	UBERON:0001911	70.30	gold quality
upper leg skin	UBERON:0004262	70.28	gold quality
right lobe of thyroid gland	UBERON:0001119	70.15	gold quality
vena cava	UBERON:0004087	69.91	gold quality
ectocervix	UBERON:0012249	69.87	gold quality
esophagus	UBERON:0001043	69.82	gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 16.

Experiment	Marker?	Max mean expression
E-HCAD-36	yes	643.08
E-MTAB-9841	yes	590.54
E-CURD-6	yes	219.45
E-MTAB-6701	yes	111.35
E-HCAD-1	yes	88.03
E-MTAB-8142	yes	84.03
E-MTAB-10553	yes	54.61
E-CURD-122	yes	40.19
E-MTAB-8410	yes	39.77
E-GEOD-135922	yes	35.44
E-HCAD-10	yes	29.12
E-CURD-112	yes	28.02
E-HCAD-9	yes	26.20
E-HCAD-11	yes	22.93
E-MTAB-10042	yes	8.96

HPA expression

RNA tissue specificity: Group enriched

showing 60 of 75 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Lymph node	tissue	265.6	medium
Tonsil	tissue	240.5	medium
Spleen	tissue	150.7	low
Bone marrow	tissue	140.1	low
Thymus	tissue	129.4
Appendix	tissue	108.8	medium
Urinary bladder	tissue	39.2	not detected
Stomach 1	tissue	30.6	not detected
Rectum	tissue	30.5	not detected
Small intestine	tissue	29.3	not detected
Lung	tissue	29.2	not detected
Gallbladder	tissue	24.9	not detected
Colon	tissue	23.3	not detected
Duodenum	tissue	19.3	not detected
Liver	tissue	18.5	not detected
Breast	tissue	17.5	not detected
Salivary gland	tissue	13.2	not detected
Smooth muscle	tissue	11.7	not detected
Adipose tissue	tissue	11.0	not detected
Cervix	tissue	9.6	not detected
Esophagus	tissue	7.9	not detected
Prostate	tissue	7.6	not detected
Spinal cord	tissue	7.3
Endometrium 1	tissue	6.3	not detected
Corpus callosum	tissue	6.2
Adrenal gland	tissue	5.6	not detected
Placenta	tissue	5.4	not detected
Fallopian tube	tissue	5.4	not detected
Medulla oblongata	tissue	5.2
Substantia nigra	tissue	5.2
Vagina	tissue	4.8	not detected
Midbrain	tissue	4.8
Epididymis	tissue	4.7	not detected
Thyroid gland	tissue	4.4	not detected
Seminal vesicle	tissue	4.1	not detected
Olfactory bulb	tissue	4.1
Heart muscle	tissue	4.0	not detected
Periaqueductal gray	tissue	4.0
Thalamus	tissue	3.7
Hypothalamus	tissue	3.7
Pons	tissue	3.6
Kidney	tissue	3.6	not detected
Septum	tissue	3.6
Superior colliculi	tissue	3.5
Skin 1	tissue	3.3	not detected
Putamen	tissue	3.3
Hippocampal formation	tissue	3.3
Ventral forebrain	tissue	3.3
Tongue	tissue	3.2
Basal ganglia	tissue	3.1	not detected
Amygdala	tissue	3.1
Testis	tissue	2.7	not detected
Skeletal muscle	tissue	2.7	not detected
Cerebellum	tissue	2.7	not detected
Entorhinal cortex	tissue	2.7
Cerebral cortex	tissue	2.6	not detected
Ovary	tissue	2.6	not detected
Retrosplenial and cingulate cortex	tissue	2.6
Retrosplenial cortex	tissue	2.6
Temporal cortex	tissue	2.6

Brain sub-regions (HPA Brain Atlas): detected in 186; highest nTPM — Dorsal spinal cord (7.3), Ventral spinal cord (6.9), Blood vessel (6.8), White matter (6.2), Lateral funiculus (white matter) (5.9).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CD48 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 31 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-3675-3P	99.09	67.70	968
HSA-MIR-4424	98.91	70.33	1145
HSA-MIR-6755-3P	98.61	66.90	834
HSA-MIR-31-5P	98.58	68.35	1239
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-3074-3P	97.83	67.26	922

Functional genomics

gnomAD constraint: pLI 5.03e-07, LOEUF 1.31, missense Z -0.062 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000368046 — one region, missense o/e 1.07.

Literature-anchored findings (GeneRIF, showing 37)

• The Drosophila miR-959-962 Cluster Members Repress Toll Signaling to Regulate Antibacterial Defense during Bacterial Infection. (PMID:33477373)
• CM1-induced apoptosis is achieved via different initiation pathways, which are cell-type dependent (PMID:12072193)
• Signal-dependent adhesion of resting NK cells initiated by expression of ICAM-1 is greatly enhanced by coexpression of CD48, even in the absence of cytokines. (PMID:12496412)
• Engagement of natural killer (NK) cell receptor 2B4 by its counterreceptor, CD48, expressed on target cells leads to an inhibition in NK cytotoxicity independent of signaling lymphocytic activation molecule-associated protein (SAP) expression. (PMID:15356144)
• IL-18, IL-18 receptor alpha, and CD48 complex formation via glycosylphosphatidylinositol anchor glycan triggers binding to IL-18 receptor beta, and thereby induces intracellular signal transduction and IFN-gamma production. (PMID:15760905)
• Review of recent studies suggests an important role for interactions between 2B4 and CD48 in the course of T cell activation and proliferation (PMID:16081768)
• 2B4 (CD244) can stimulate NK cell cytotoxicity and cytokine production by interacting with NK cell expressed CD48 and adds CD48 to the growing number of activating NK cell receptors (PMID:16585556)
• CD48 is an interleukin (IL)-3-induced activating receptor on eosinophils and may be involved in promoting allergic inflammation. (PMID:16785501)
• CD48 is a CD2 and CD244 (2B4)-binding protein (PMID:16803907)
• In conclusion, we cannot confirm a role of human endogenous retrovirus-K18 superantigen polymorphisms or of the CD48 CA repeat for type 1 diabetes susceptibility. (PMID:16866884)
• findings indicate that FimH induces host cell signalling cascades that are involved in E. coli K1 invasion of human brain microvascular endothelial cells (HBMEC) and CD48 is a putative HBMEC receptor for FimH (PMID:17222190)
• the mechanism of signal transduction by CD244 is to regulate FYN kinase recruitment and/or activity and the outcome of CD48/CD244 interactions is determined by which other receptors are engaged. (PMID:17599905)
• CD2 functions as the master switch recruiting CD48 and Lck (PMID:19494291)
• The ligand (CD48) of the 2B4 receptor can exert both activating and inhibiting signals; natural killer (NK) cells might be at risk for self-killing were it not for the inhibiting signals generated by the 2B4-CD48 interaction. (PMID:20164429)
• Stimulation of CD48 induces rearrangement of signaling factors in lipid rafts, Lck-kinase activity, and tyrosine phosphorylation. (PMID:20833258)
• replication study of association of 2 SNPs in HERV-K18 and 19 tagSNPs in CD48 with schizophrenia (SZ)and type 2 diabetes (T2D) in patients with SZ in 2 Danish samples; no association was found with SZ or with T2D among individuals with SZ for any of the SNPs (PMID:22495247)
• Monocyte-induced natural killer cell dysfunction was markedly attenuated by blocking CD48 receptor 2B4 on NK cells, but not by blockade of NKG2D and NKp30. (PMID:23225218)
• Blockade of 2B4/CD48 interaction resulted in improvement in function via perforin expression and degranulation as measured by CD107a surface mobilization on HTLV-1 specific CD8+ T cells. (PMID:24505299)
• we propose that SLAMF2 engagement regulates adaptive immune responses (PMID:24670806)
• These data demonstrate the important role of CD48 in SA/exotoxins-eosinophil activating interactions that can take place during allergic responses and indicate CD48 as a novel therapeutic target for allergy and especially of AD. (PMID:25255823)
• Our data indicate sCD48 as a SEB-induced ‘decoy’ receptor derived from eosinophil and therefore as a potential anti-inflammatory tool in S. aureus-induced eosinophil inflammation often associated with allergy. (PMID:26836239)
• The present study provides further insights into the role of the 2B4-CD48 interaction in the fine regulation of CD8(+) T-cell effector function upon antigenic stimulation. (PMID:26860368)
• CD48 expression was increased in patients with a short disease duration compared to both controls and patients with longer disease duration. In patients with short disease duration, increased CD48 expression was associated with alveolar inflammation. (PMID:26926492)
• Data show that 2B4 not only can bind to CD48 in trans but also interacts with CD48 in cis by using the same binding interface. Also, the results demonstrated that constitutive phosphorylation of 2B4 occurs only in the presence of CD48, and that cis binding is sufficient to induce substantial levels of baseline phosphorylation. (PMID:27249817)
• mCD48 and sCD48 are differentially expressed in the peripheral blood of asthma patients of varying severity. sCD48 inhibits CD244-mediated eosinophil activation. These findings suggest that CD48 may play an important role in human asthma. (PMID:27859399)
• soluble CD48 levels were significantly elevated in patients with nonallergic asthma compared to control and to the allergic asthma cohort (PMID:30306094)
• immune receptor CD48 is overexpressed on MM cells together with SLAMF7, and that CD48 may be considered as an alternative target for treatment of MM in cases showing weak expression of SLAMF7. (PMID:31115879)
• this study demonstrates recurrent inflammatory disease caused by a heterozygous mutation in CD48 (PMID:31419545)
• CD48 mRNA expression was significantly lower in patients than in normal healthy individuals. (PMID:31922199)
• Human innate lymphoid cell precursors express CD48 that modulates ILC differentiation through 2B4 signaling. (PMID:33219153)
• sCD48 is elevated in non-allergic but not in allergic persistent rhinitis. (PMID:34477021)
• GDF15 induces immunosuppression via CD48 on regulatory T cells in hepatocellular carcinoma. (PMID:34489334)
• Elevated levels of sCD48 are inversely correlated with markers of disease activity in bullous pemphigoid. (PMID:36134505)
• Patients with coronavirus disease 2019 characterized by dysregulated levels of membrane and soluble cluster of differentiation 48. (PMID:36280100)
• Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer’s disease. (PMID:36520044)
• Programmed Cell Death-1 (PD-1) anchoring to the GPI-linked co-receptor CD48 reveals a novel mechanism to modulate PD-1-dependent inhibition of human T cells. (PMID:36889184)
• CD48 suppresses proliferation and migration as an immune-related prognostic signature in the cervical cancer immune microenvironment. (PMID:37279525)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cd58	ENSDARG00000098461
mus_musculus	Cd48	ENSMUSG00000015355
rattus_norvegicus	Cd48	ENSRNOG00000004737

Paralogs (9): SLAMF7 (ENSG00000026751), CD84 (ENSG00000066294), CD2 (ENSG00000116824), SLAMF1 (ENSG00000117090), CD244 (ENSG00000122223), LY9 (ENSG00000122224), SLAMF8 (ENSG00000158714), SLAMF9 (ENSG00000162723), SLAMF6 (ENSG00000162739)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:88339) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 3 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal T cell activation	1
decreased T cell proliferation	1
increased CD4-positive, alpha-beta T cell number	1

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CD84-AS1	ncRNA	105371468
SLAMF7	protein-coding	57823
SLAMF1	protein-coding	6504
CD84	protein-coding	8832
LY9	protein-coding	4063
CD244	protein-coding	51744
SLAMF6	protein-coding	114836

Protein

Protein identifiers

CD48 antigen — P09326 (reviewed: P09326)

Alternative names: B-lymphocyte activation marker BLAST-1, BCM1 surface antigen, Leukocyte antigen MEM-102, SLAM family member 2, Signaling lymphocytic activation molecule 2, TCT.1

All UniProt accessions (2): A0A087X1S7, P09326

UniProt curated annotations — full annotation on UniProt →

Function. Glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein that interacts via its N-terminal immunoglobulin domain with cell surface receptors including CD244/2B4 or CD2 to regulate immune cell function and activation. Participates in T-cell signaling transduction by associating with CD2 and efficiently bringing the Src family protein kinase LCK and LAT to the TCR/CD3 complex. In turn, promotes LCK phosphorylation and subsequent activation. Induces the phosphorylation of the cytoplasmic immunoreceptortyrosine switch motifs (ITSMs) of CD244 initiating a series of signaling events that leads to the generation of the immunological synapse and the directed release of cytolytic granules containing perforin and granzymes by T-lymphocytes and NK-cells.

Subunit / interactions. Interacts with CD2. Interacts with CD244; this interaction is possible not only on different cells (trans interaction) but also on the same cell (cis interaction). Interacts with LCK.

Subcellular location. Cell membrane. Membrane raft. Secreted.

Tissue specificity. Widely expressed on all hematopoietic cells.

Induction. By IFN-alpha/beta and IFN-gamma both at the level of CD48 mRNA and cell surface expression.

Isoforms (2)

UniProt ID	Names	Canonical?
P09326-1	1	yes
P09326-2	2

RefSeq proteins (2): NP_001242959, NP_001769* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR015631	CD2/SLAM_rcpt	Family
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF07686, PF13895

UniProt features (31 total): strand 9, glycosylation site 5, turn 3, splice variant 2, sequence variant 2, sequence conflict 2, domain 2, signal peptide 1, chain 1, disulfide bond 1, propeptide 1, helix 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
2EDO	Solution structure of the first ig-like domain from human CD48 antigen	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P09326-F1	83.20	0.61

Human Protein Atlas

Protein class: CD markers, Transporters, Accessory Factors Involved in Transport, Predicted membrane proteins, Predicted secreted proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): plasma membrane; cytosol; nucleoli fibrillar center

Antibody reliability (HPA): IH enhanced · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1)

Type	Positions
Gpi-anchor amidated serine	220

Disulfide bonds (1)

Type	Positions
Disulfide bond	154–196

Glycosylation sites (5)

Type	Positions
N-linked (glcnac…) asparagine	189, 40, 44, 104, 162

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 2; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

2 pathways:

ID	Pathway	Evidence
R-HSA-202733	Cell surface interactions at the vascular wall	curated
R-HSA-109582	Hemostasis	—

MSigDB gene sets: 315 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, WALLACE_PROSTATE_CANCER_RACE_UP, MCLACHLAN_DENTAL_CARIES_UP, MODULE_45, CROONQUIST_NRAS_SIGNALING_UP, WIELAND_UP_BY_HBV_INFECTION, GOLDRATH_ANTIGEN_RESPONSE, MODULE_75, FINAK_BREAST_CANCER_SDPP_SIGNATURE, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, MODULE_171, GOBP_NATURAL_KILLER_CELL_ACTIVATION, SANSOM_APC_TARGETS_DN, BROWN_MYELOID_CELL_DEVELOPMENT_DN, SABATES_COLORECTAL_ADENOMA_DN

GO Biological Process (5): defense response (GO:0006952), immune response (GO:0006955), natural killer cell activation (GO:0030101), signal transduction (GO:0007165), leukocyte activation (GO:0045321)

GO Molecular Function (2): receptor ligand activity (GO:0048018), protein binding (GO:0005515)

GO Cellular Component (6): plasma membrane (GO:0005886), membrane (GO:0016020), membrane raft (GO:0045121), extracellular exosome (GO:0070062), side of membrane (GO:0098552), extracellular region (GO:0005576)

Reactome top-level categories

1 top-level categories:

Category	Pathways
Hemostasis	1

GO top-level categories

20 GO namespaces:

Category	Terms
cellular anatomical structure	3
immune system process	2
membrane	2
response to stress	1
response to stimulus	1
lymphocyte activation	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
cell activation	1
signaling receptor binding	1
signal transduction	1
signaling receptor activator activity	1
binding	1
cell periphery	1
membrane microdomain	1
extracellular vesicle	1
leaflet of membrane bilayer	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO term	NS	Evidence
natural killer cell activation	BP	direct assay
extracellular exosome	CC	high-throughput assay
membrane	CC	high-throughput assay
membrane raft	CC	direct assay
receptor ligand activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 2,226 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD48	LY9	Q9HBG7	914
CD48	CD84	Q9UIB8	860
CD48	CD244	Q9BZW8	860
CD48	CD2	P06729	845
CD48	SLAMF6	Q96DU3	807
CD48	KIT	P10721	806
CD48	MATK	P42679	799
CD48	FLT3	P36888	779
CD48	SH2D1A	O60880	773
CD48	SLAMF7	Q9NQ25	765
CD48	LCK	P06239	752
CD48	NCR1	O76036	749
CD48	CD58	P19256	748
CD48	CD34	P28906	713
CD48	PTPRC	P08575	689

IntAct

Human interaction partners of CD48 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

5 partners by confidence:

Partner	Interaction type	MIscore	Records
CD244	physical association	0.790	5
PRAP1	association	0.530	1
POTEF	association	0.350	1
BXDC2	physical association	0.000	1
EEF1D	physical association	0.000	1

BioGRID (36 interactions; top human partners by supporting records): PRAP1 (Affinity Capture-MS; 3 records), ADAM21 (Affinity Capture-MS), BRIX1 (Two-hybrid), CBWD3 (Affinity Capture-MS), CD2 (Reconstituted Complex), CLSTN1 (Affinity Capture-MS), CTHRC1 (Affinity Capture-MS), EEF1D (Two-hybrid), FBXO2 (Affinity Capture-MS), GPR107 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), IGF1R (Affinity Capture-MS), LAMB1 (Affinity Capture-MS), LAMB2 (Affinity Capture-MS), LAMC1 (Affinity Capture-MS)

Ligand–receptor pairs (CellPhoneDB) (1)

Curated ligand–receptor partners (cell-cell communication), distinct from the protein–protein interactions above.

1 ligand–receptor pairs:

Partner	This gene’s role	Signaling class
CD244	ligand

Disease & clinical

Genetic variants

Variant evidence for CD48: 55 ClinVar records (0 pathogenic / likely pathogenic); 5 GWAS associations.

ClinVar

55 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	4
Benign	7

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 19 predictions of 522):

Position(s)	Effect	Δscore	Sites
1:160711680–160711681	donor_loss	0.9900	5
1:160698232	donor_gain	0.9700
1:160711680	donor_loss	0.9700
1:160711693	donor_gain	0.9500
1:160680045	acceptor_gain	0.9400
1:160685051	donor_gain	0.9400
1:160681380	donor_gain	0.9200
1:160704387	donor_gain	0.9200
1:160711682	donor_loss	0.9200
1:160681469–160681470	acceptor_loss	0.8800	6

AlphaMissense

211 missense substitutions predicted likely pathogenic (of 1,594 scored), across 67 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
D103	8	0.915	0.967
C154	7	0.943	0.964
C196	7	0.936	0.970
W58	7	0.913	0.977
W165	7	0.907	0.983
F81	7	0.872	0.932
C148	7	0.788	0.840
N200	7	0.784	0.948
C215	7	0.768	0.854
F77	6	0.798	0.936
V127	6	0.798	0.906
Y107	5	0.932	0.976
S203	5	0.844	0.931
F59	5	0.796	0.819
R84	5	0.772	0.884
K65	5	0.762	0.891
E68	5	0.591	0.609
I66	4	0.792	0.887
S105	4	0.735	0.758
G92	4	0.694	0.806

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Lung Adenocarcinoma (TCGA)	favorable	0.000312
Breast Invasive Carcinoma (TCGA)	favorable	0.000581

Disease associations

OMIM: gene MIM:109530 | disease phenotypes:

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (1 panels, 0 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

1 panels:

Panel	Rating
Primary immunodeficiency or monogenic inflammatory bowel disease	amber

GWAS associations

5 associations:

Study	Trait	p-value
GCST006585_2236	Blood protein levels	5e-19
GCST009597_136	Multiple sclerosis	6e-16
GCST001725_36	Inflammatory bowel disease	7e-9
GCST004861_6	Itch intensity from mosquito bite	2e-8
GCST004068_43	Venous thromboembolism adjusted for sickle cell variant rs77121243-T	5e-7

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0008377	mosquito bite reaction itch intensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	4
Nickel	increases expression	2
GSK-J4	increases expression	1
terbufos	increases methylation	1
sodium arsenite	affects methylation	1
manganese chloride	increases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
4-hydroxy-equilenin	increases expression	1
CGP 52608	affects binding, increases reaction	1
cotylenin A	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Benzoates	increases expression	1
Carbamazepine	affects expression	1
Cisplatin	increases expression	1
Demecolcine	increases expression	1
Diuron	decreases expression	1
Dust	increases expression	1
Fonofos	increases methylation	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Manganese	increases expression	1
Methotrexate	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Parathion	increases methylation	1
Tretinoin	increases expression	1
Vincristine	increases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases expression	1
beta-Naphthoflavone	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B7WI	Abcam Raji CD48 KO	Cancer cell line	Male
CVCL_B9X3	Abcam THP-1 CD48 KO	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.