CD72

gene
On this page

Also known as LYB2CD72b

Summary

CD72 (CD72 molecule, HGNC:1696) is a protein-coding gene on chromosome 9p13.3, encoding B-cell differentiation antigen CD72 (P21854). Co-receptor of B cell receptor (BCR) that plays both positive and negative roles on B-cell functions.

Enables transmembrane signaling receptor activity. Involved in negative regulation of B cell receptor signaling pathway. Located in plasma membrane.

Source: NCBI Gene 971 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 50 total
  • Druggable target: yes
  • MANE Select transcript: NM_001782

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1696
Approved symbolCD72
NameCD72 molecule
Location9p13.3
Locus typegene with protein product
StatusApproved
AliasesLYB2, CD72b
Ensembl geneENSG00000137101
Ensembl biotypeprotein_coding
OMIM107272
Entrez971

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding_CDS_not_defined, 4 protein_coding

ENST00000259633, ENST00000378430, ENST00000378431, ENST00000396757, ENST00000463720, ENST00000465754, ENST00000470387, ENST00000477364, ENST00000482121, ENST00000490239

RefSeq mRNA: 1 — MANE Select: NM_001782 NM_001782

CCDS: CCDS6581

Canonical transcript exons

ENST00000259633 — 9 exons

ExonStartEnd
ENSE000015261583560998235610300
ENSE000015261623561822235618413
ENSE000034617773561284835612993
ENSE000034744873561594335616278
ENSE000034974403561060235610753
ENSE000035452913561801435618121
ENSE000035585413561717635617247
ENSE000036330003561180435611919
ENSE000036572733561660035616689

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 96.69.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9198 / max 223.3429, expressed in 800 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1005851.2476142
1005900.9232551
1005890.5159232
1005870.099851
2054720.057224
1005910.039116
1005860.037016

Top tissues by expression

285 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spleenUBERON:000210696.69gold quality
lymph nodeUBERON:000002991.58gold quality
granulocyteCL:000009491.14gold quality
vermiform appendixUBERON:000115490.48gold quality
caecumUBERON:000115383.40gold quality
bloodUBERON:000017882.35gold quality
bone marrowUBERON:000237179.92gold quality
tonsilUBERON:000237279.88gold quality
gall bladderUBERON:000211079.80gold quality
small intestine Peyer’s patchUBERON:000345479.13gold quality
superficial temporal arteryUBERON:000161477.27gold quality
right uterine tubeUBERON:000130277.08gold quality
right lungUBERON:000216777.05gold quality
adenohypophysisUBERON:000219676.94gold quality
right adrenal gland cortexUBERON:003582775.80gold quality
Brodmann (1909) area 10UBERON:001354175.69gold quality
bone marrow cellCL:000209275.68gold quality
right adrenal glandUBERON:000123375.64gold quality
leukocyteCL:000073875.52gold quality
epithelium of nasopharynxUBERON:000195175.32gold quality
descending thoracic aortaUBERON:000234575.25gold quality
small intestineUBERON:000210875.22gold quality
left adrenal gland cortexUBERON:003582575.18gold quality
islet of LangerhansUBERON:000000674.78gold quality
left adrenal glandUBERON:000123474.66gold quality
type B pancreatic cellCL:000016974.56gold quality
mononuclear cellCL:000084274.40gold quality
monocyteCL:000057674.39gold quality
mucosa of stomachUBERON:000119974.28gold quality
endometrium epitheliumUBERON:000481173.94gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-CURD-122yes67.72
E-HCAD-4yes55.16
E-CURD-112yes41.90
E-MTAB-9067yes17.11
E-ANND-3yes15.07
E-HCAD-10yes13.52
E-MTAB-9801yes5.43
E-MTAB-6386no1605.08

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, PAX5, SPI1

miRNA regulators (miRDB)

15 targeting CD72, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-95-5P99.8972.173973
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-148A-3P99.7473.771700
HSA-MIR-148B-3P99.7473.751700
HSA-MIR-152-3P99.7473.751703
HSA-MIR-6840-3P98.6865.951923
HSA-MIR-5088-3P98.2966.631310
HSA-MIR-6842-3P98.0766.331325
HSA-MIR-365297.7165.431890
HSA-MIR-443097.4765.611813

Literature-anchored findings (GeneRIF, showing 18)

  • results indicated that the presence of CD72-*2 allele decreases risk for human systemic lupus erythematosus conferred by FCGR2B-232Thr, possibly by increasing the AS isoform of CD72 (PMID:15459183)
  • CD72 is a key molecule in regulating mature B cell differentiation; CD72 signaling reduces the expression of X-box binding protein 1 in B cells (PMID:16047337)
  • increased nucleotide mutation of CD72 mRNA accounts for the decreased expression level of CD72 in B cells, and it might be related to hyperactivity of B cells in patients with SLE (PMID:17121583)
  • CD100-CD72 interaction can be the mechanism by which NK cell communicate with B cells. (PMID:17786190)
  • CD72 polymorphisms are associated with age of appearing clinical manifestations in idiopathic thrombocytopenic purpura in Chinese patients. (PMID:18071878)
  • Data show that ligation of CD72 with the BU40, or with rCD100 negatively regulates KIT-mediated mast cell proliferation, chemotaxis, and chemokine production. (PMID:20100931)
  • CD72 mRNA expression level correlates with Sema4D expression in peripheral blood mononuclear cells in immune thrombocytopenia. (PMID:22111667)
  • data demonstrated aberrant expression of CD72 exists on B cells of myasthenia gravis and multiple sclerosis patients and expression level of CD72 molecule has a significantly negative correlation with anti-AchR antibody levels in myasthenia gravis (PMID:23184497)
  • regulates serum immunoglobulin leveln and disease resistance in systemic lupus erythematosus (PMID:23268649)
  • CD72 expression on activated B cells of SLE patients was significantly lower than that of normal controls. sema3A enhanced CD72 expression of B cells, but it was still lower in SLE patients than in normal individuals. (PMID:24461079)
  • Increased soluble CD72 in systemic lupus erythematosus is in association with disease activity and lupus nephritis (PMID:26883681)
  • Interferon-alpha-induced CD100 expression on naive CD8(+) T cells enhances antiviral responses to hepatitis C infection through CD72 signal transduction. (PMID:28222623)
  • A regulatory role for CD72 expression on B cells and increased soluble CD72 in primary Sjogren’s syndrome. (PMID:32306893)
  • CD40 and CD72 expression and prognostic values among children with systemic lupus erythematosus: a case-control study. (PMID:32700598)
  • Blockage of CD72 reduces B cell proliferation in immune thrombocytopenic purpura, involving interleukin 1 and macrophage migration inhibitory factor secretion. (PMID:36326455)
  • CD72-semaphorin3A axis: A new regulatory pathway in systemic lupus erythematosus. (PMID:36470209)
  • CD72 is a pan-tumor antigen associated to pediatric acute leukemia. (PMID:37876342)
  • CD72, a new immune checkpoint molecule, is a novel prognostic biomarker for kidney renal clear cell carcinoma. (PMID:37980541)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCd72ENSMUSG00000028459
rattus_norvegicusCd72ENSRNOG00000017485

Protein

Protein identifiers

B-cell differentiation antigen CD72P21854 (reviewed: P21854)

Alternative names: Lyb-2

All UniProt accessions (5): A0A6E1WA84, P21854, Q5T4Q7, Q5T4Q8, Q5TLG3

UniProt curated annotations — full annotation on UniProt →

Function. Co-receptor of B cell receptor (BCR) that plays both positive and negative roles on B-cell functions. Recognizes the Sm/ribonucleoprotein (RNP) self-antigen ligand, and coligation of CD72 and BCR inhibits BCR signaling. Mechanistically, ligand binding leads to the recruitment of PTPN6/SHP-1 to the BCR complex which is inhibitory to BCR signaling. Also acts as a ligand for CD5 and thereby plays a critical role in maintaining regulatory T and B-cell homeostasis.

Subunit / interactions. Homodimer; disulfide-linked. Associates with CD5. Interacts (tyrosine phosphorylated) with PTPN6/SHP-1.

Subcellular location. Membrane.

Tissue specificity. Pre-B-cells and B-cells but not terminally differentiated plasma cells.

Post-translational modifications. Phosphorylated upon engagement of the B-cell receptor, probably by LYN or SYK. Phosphorylation at Tyr-7 is important for interaction with PTPN6/SHP-1.

RefSeq proteins (1): NP_001773* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001304C-type_lectin-likeDomain
IPR016186C-type_lectin-like/link_sfHomologous_superfamily
IPR016187CTDL_foldHomologous_superfamily
IPR039689CD72Family

Pfam: PF00059

UniProt features (12 total): disulfide bond 3, topological domain 2, modified residue 2, chain 1, sequence variant 1, transmembrane region 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P21854-F176.850.48

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 (2): 7, 39

Disulfide bonds (3): 325–342, 233–244, 261–350

Glycosylation sites (1): 136

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-416700Other semaphorin interactions
R-HSA-1266738Developmental Biology
R-HSA-373755Semaphorin interactions
R-HSA-422475Axon guidance
R-HSA-9675108Nervous system development

MSigDB gene sets: 340 (showing top): PID_BCR_5PATHWAY, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_REGULATION_OF_B_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, YAGI_AML_WITH_INV_16_TRANSLOCATION, GCANCTGNY_MYOD_Q6, REACTOME_OTHER_SEMAPHORIN_INTERACTIONS, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, MORI_IMMATURE_B_LYMPHOCYTE_UP, CAGCTG_AP4_Q5, GOBP_REGULATION_OF_IMMUNE_RESPONSE, MODULE_75, ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP, chr9p13, MODULE_410

GO Biological Process (2): cell adhesion (GO:0007155), negative regulation of B cell receptor signaling pathway (GO:0050859)

GO Molecular Function (4): transmembrane signaling receptor activity (GO:0004888), signaling receptor binding (GO:0005102), carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Semaphorin interactions1
Axon guidance1
Nervous system development1
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular process1
B cell receptor signaling pathway1
regulation of B cell receptor signaling pathway1
negative regulation of antigen receptor-mediated signaling pathway1
signaling receptor activity1
protein binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

1248 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CD72SEMA4DQ92854998
CD72CD5P06127992
CD72PLXNB1O43157846
CD72FCGR2BP31994803
CD72CD22P20273795
CD72PTPN6P29350719
CD72SEMA4AQ9H3S1676
CD72PLXNB2O15031624
CD72CD79AP11912622
CD72CD79BP40259586
CD72FCRLAQ7L513572
CD72CD19P15391552
CD72CHIAQ9BZP6552
CD72CD6P30203550
CD72CR2P20023532

IntAct

54 interactions, top by confidence:

ABTypeScore
CD72CGRRF1psi-mi:“MI:0915”(physical association)0.560
CD72LHFPL5psi-mi:“MI:0915”(physical association)0.560
CD72SPACA1psi-mi:“MI:0915”(physical association)0.560
CD72ATP6AP2psi-mi:“MI:0915”(physical association)0.560
CD72GRAMD1Cpsi-mi:“MI:0915”(physical association)0.560
CD72BIKpsi-mi:“MI:0915”(physical association)0.560
CD72NRG1psi-mi:“MI:0915”(physical association)0.560
CD72LSMEM2psi-mi:“MI:0915”(physical association)0.560
CD72CREB3L1psi-mi:“MI:0915”(physical association)0.560
CD72MS4A7psi-mi:“MI:0915”(physical association)0.560
CLDN7CD72psi-mi:“MI:0915”(physical association)0.560
CD72LRRC25psi-mi:“MI:0915”(physical association)0.560
CD72GPR152psi-mi:“MI:0915”(physical association)0.560
CD72MS4A3psi-mi:“MI:0915”(physical association)0.560
ATP6AP2CD72psi-mi:“MI:0915”(physical association)0.560
SEMA4DCD72psi-mi:“MI:0407”(direct interaction)0.440
HMGA1CD72psi-mi:“MI:0915”(physical association)0.400
CD5CD72psi-mi:“MI:0915”(physical association)0.400
CD72TRUB1psi-mi:“MI:0915”(physical association)0.400
CD72NCAM2psi-mi:“MI:0915”(physical association)0.400
FCGR2ACD72psi-mi:“MI:0915”(physical association)0.400
FCGR1ACD72psi-mi:“MI:0915”(physical association)0.400
CD72CALML3psi-mi:“MI:0914”(association)0.350

BioGRID (33): CD72 (Reconstituted Complex), SIGLEC10 (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CD72 (Two-hybrid), CD72 (Affinity Capture-Western), CD72 (Affinity Capture-Western), CD72 (Two-hybrid), CD72 (Two-hybrid), CD72 (Two-hybrid), MS4A3 (Two-hybrid), NRG1 (Two-hybrid), CREB3L1 (Two-hybrid), MS4A7 (Two-hybrid), LRRC25 (Two-hybrid)

ESM2 similar proteins: A4KWA1, D4AD02, O70156, O70215, P20937, P21854, P21855, P26715, P26717, P27471, P27811, P27812, P27814, P60883, Q149M0, Q2HXU8, Q2NL33, Q504P2, Q5QGZ9, Q60651, Q60652, Q60653, Q60654, Q60660, Q60682, Q64329, Q6QLQ4, Q6UXN8, Q6WRU0, Q80ZC8, Q8BRU4, Q8BWY2, Q8CJC7, Q8HY02, Q8HY04, Q8HY06, Q8MI05, Q8NC01, Q8VBX4, Q8VD98

Diamond homologs: A4KWA5, A4KWA8, O88713, O89335, P06734, P0CA63, P0CA64, P14370, P14371, P21854, P26715, Q0H8B9, Q5M9I1, Q64329, Q64335, Q65150, Q6ZS10, Q80XD9, Q8C1T8, Q8CJC7, Q8VI21, Q91V08, Q92478, Q925N7, Q9D676, Q9MZJ3, Q9R0Q8, Q9UHP7, P07307, P21855, P34927, P49300, P49301, Q69FH1, Q8HZR8, Q8IUN9, Q9BXN2, A4KWA6, A6QP79, D3W0D1

SIGNOR signaling

1 interactions.

AEffectBMechanism
PTPN6down-regulatesCD72dephosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1423 predictions. Top by Δscore:

VariantEffectΔscore
9:35612846:A:ACdonor_gain0.9900
9:35612847:C:CCdonor_gain0.9900
9:35617174:A:ACdonor_gain0.9900
9:35617175:C:CCdonor_gain0.9900
9:35617245:CCG:Cacceptor_gain0.9900
9:35617246:CG:Cacceptor_gain0.9900
9:35617246:CGC:Cacceptor_gain0.9900
9:35617248:C:CCacceptor_gain0.9900
9:35618076:TGA:Tdonor_gain0.9900
9:35619511:CCA:Cdonor_gain0.9900
9:35615937:GGATA:Gdonor_loss0.9800
9:35615938:GATA:Gdonor_loss0.9800
9:35615939:ATAC:Adonor_loss0.9800
9:35615940:TA:Tdonor_loss0.9800
9:35615941:A:Cdonor_loss0.9800
9:35615942:CCTG:Cdonor_gain0.9800
9:35616594:A:ACdonor_gain0.9800
9:35616595:C:CCdonor_gain0.9800
9:35618220:AC:Adonor_gain0.9800
9:35618221:CC:Cdonor_gain0.9800
9:35612915:T:Adonor_gain0.9700
9:35616599:CAG:Cdonor_gain0.9700
9:35616599:CAGCG:Cdonor_gain0.9700
9:35616691:T:Cacceptor_gain0.9700
9:35617247:GC:Gacceptor_loss0.9700
9:35617248:CTGT:Cacceptor_loss0.9700
9:35617249:T:Cacceptor_loss0.9700
9:35618016:G:Adonor_gain0.9700
9:35619506:CCTCA:Cdonor_loss0.9700
9:35619507:CTCAC:Cdonor_loss0.9700

AlphaMissense

2308 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:35612971:C:AW237C0.997
9:35612971:C:GW237C0.997
9:35612973:A:GW237R0.994
9:35612973:A:TW237R0.994
9:35612900:C:GC261S0.993
9:35612901:A:TC261S0.993
9:35618268:A:CF12L0.992
9:35618268:A:TF12L0.992
9:35618270:A:GF12L0.992
9:35610655:C:GC350S0.991
9:35610656:A:TC350S0.991
9:35611860:C:AW298C0.991
9:35611860:C:GW298C0.991
9:35610655:C:TC350Y0.987
9:35612899:A:CC261W0.986
9:35610654:A:CC350W0.985
9:35612900:C:TC261Y0.985
9:35612950:G:CC244W0.985
9:35612911:G:CS257R0.984
9:35612911:G:TS257R0.984
9:35612913:T:GS257R0.984
9:35612951:C:GC244S0.984
9:35612952:A:TC244S0.984
9:35612920:C:AW254C0.983
9:35612920:C:GW254C0.983
9:35612900:C:AC261F0.982
9:35612901:A:GC261R0.982
9:35612951:C:TC244Y0.982
9:35612952:A:GC244R0.982
9:35610656:A:GC350R0.977

dbSNP variants (sampled 300 via entrez): RS1000058731 (9:35638800 G>A,C), RS1000096557 (9:35632070 C>G), RS1000105675 (9:35640585 A>G), RS1000513122 (9:35610046 G>A,T), RS1000528127 (9:35615217 G>A), RS1000561031 (9:35640332 C>T), RS1000566923 (9:35610234 G>A,C,T), RS1000659432 (9:35637423 C>T), RS1000718185 (9:35646194 G>T), RS1000747793 (9:35645800 C>T), RS1000793277 (9:35629435 ATATG>A), RS1000816561 (9:35611344 C>T), RS1000968625 (9:35623323 G>A,C), RS1001093015 (9:35637250 C>T), RS1001103118 (9:35630451 C>G)

Disease associations

OMIM: gene MIM:107272 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002709_10Electroencephalogram traits2.000000e-06
GCST006585_664Blood protein levels5.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004357electroencephalogram measurement
EFO:0006870alpha wave measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5169122 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
GSK-J4decreases expression1
sotorasibaffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
titanium dioxideincreases expression1
terbufosincreases methylation1
sodium arseniteincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
di-n-butylphosphoric acidaffects expression1
ON 01910decreases expression1
trametinibaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
NVP-BKM120affects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsdecreases methylation, increases abundance1
Arsenicaffects methylation1
Atrazineincreases expression1
Benzo(a)pyrenedecreases expression1
Fonofosincreases methylation1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression1
Nitrogen Dioxidedecreases methylation, increases abundance1
Oxygenincreases expression1
Parathionincreases methylation1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Antirheumatic Agentsdecreases expression1
Okadaic Aciddecreases expression1
Permethrinincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5136271BindingInduction of CD72 degradation in human MINO cells at 100 nM measured after 8 hrs by proteomic analysisStructural Feature Analyzation Strategies toward Discovery of Orally Bioavailable PROTACs of Bruton’s Tyrosine Kinase for the Treatment of Lymphoma. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E1JSHyCyte Daudi KO-hCD72Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.