B2M

gene
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Summary

B2M (beta-2-microglobulin, HGNC:914) is a protein-coding gene on chromosome 15q21.1, encoding Beta-2-microglobulin (P61769). Component of the class I major histocompatibility complex (MHC). In precision oncology, B2M S14FS is associated with resistance to Pembrolizumab in Skin Melanoma (CIViC Level C).

This gene encodes a serum protein found in association with the major histocompatibility complex (MHC) class I heavy chain on the surface of nearly all nucleated cells. The protein has a predominantly beta-pleated sheet structure that can form amyloid fibrils in some pathological conditions. The encoded antimicrobial protein displays antibacterial activity in amniotic fluid. A mutation in this gene has been shown to result in hypercatabolic hypoproteinemia.

Source: NCBI Gene 567 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): hypoproteinemia, hypercatabolic (Strong, GenCC) — +3 more curated relationships
  • Clinical variants (ClinVar): 104 total — 2 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 51
  • Druggable target: yes
  • Precision-oncology evidence (CIViC): 1 curated variant–drug association
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 7 cancer types
  • MANE Select transcript: NM_004048

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:914
Approved symbolB2M
Namebeta-2-microglobulin
Location15q21.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000166710
Ensembl biotypeprotein_coding
OMIM109700
Entrez567

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 5 protein_coding, 4 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000349264, ENST00000557901, ENST00000559720, ENST00000559907, ENST00000559916, ENST00000560556, ENST00000560681, ENST00000561139, ENST00000561424, ENST00000623550, ENST00000648006, ENST00000695792, ENST00000906076, ENST00000906077, ENST00000916438

RefSeq mRNA: 1 — MANE Select: NM_004048 NM_004048

CCDS: CCDS10113

Canonical transcript exons

ENST00000617605 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3314.2823 / max 69373.7594, expressed in 1828 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1463823309.70161828
1463853.49371066
1463831.0870524

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.99gold quality
monocyteCL:000057699.99gold quality
leukocyteCL:000073899.99gold quality
vermiform appendixUBERON:000115499.99gold quality
gall bladderUBERON:000211099.99gold quality
lymph nodeUBERON:000002999.98gold quality
rectumUBERON:000105299.97gold quality
spleenUBERON:000210699.97gold quality
right lungUBERON:000216799.97gold quality
upper lobe of left lungUBERON:000895299.97gold quality
stromal cell of endometriumCL:000225599.96gold quality
bloodUBERON:000017899.96gold quality
calcaneal tendonUBERON:000370199.96gold quality
islet of LangerhansUBERON:000000699.95gold quality
adipose tissueUBERON:000101399.95gold quality
smooth muscle tissueUBERON:000113599.95gold quality
placentaUBERON:000198799.95gold quality
subcutaneous adipose tissueUBERON:000219099.95gold quality
mucosa of transverse colonUBERON:000499199.95gold quality
left lobe of thyroid glandUBERON:000112099.94gold quality
right adrenal glandUBERON:000123399.94gold quality
endometriumUBERON:000129599.94gold quality
thyroid glandUBERON:000204699.94gold quality
duodenumUBERON:000211499.94gold quality
bone marrowUBERON:000237199.94gold quality
small intestine Peyer’s patchUBERON:000345499.94gold quality
olfactory segment of nasal mucosaUBERON:000538699.94gold quality
omental fat padUBERON:001041499.94gold quality
metanephros cortexUBERON:001053399.94gold quality
right lobe of thyroid glandUBERON:000111999.93gold quality

Single-cell (SCXA)

Detected in 74 experiment(s), a significant marker in 45.

ExperimentMarker?Max mean expression
E-MTAB-8207yes55889.65
E-GEOD-149689yes30093.16
E-MTAB-8142yes28703.09
E-HCAD-11yes25987.74
E-MTAB-6701yes25432.67
E-HCAD-1yes22948.43
E-MTAB-8410yes22850.40
E-GEOD-134144yes22473.89
E-MTAB-6678yes20925.40
E-HCAD-4yes19751.59
E-CURD-46yes18300.12
E-GEOD-130148yes17454.17
E-CURD-79yes16968.50
E-MTAB-7407yes16901.82
E-MTAB-10885yes15310.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYB, MYC, NFKB1, NFKB2, RELA, SPI1, TP53, USF1, USF2

miRNA regulators (miRDB)

47 targeting B2M, 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-340-5P100.0072.504437
HSA-MIR-56899.9869.862084
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-314399.9371.963104
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-449599.8272.083080
HSA-MIR-451799.7669.191867
HSA-MIR-3679-3P99.6469.881599
HSA-MIR-211399.5871.221521
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-6833-5P99.5068.931161
HSA-MIR-5590-3P99.4870.912429
HSA-MIR-142-5P99.4870.922416
HSA-MIR-469699.4867.481040
HSA-MIR-16-2-3P99.2970.601954
HSA-MIR-195-3P99.2970.611954

Literature-anchored findings (GeneRIF, showing 40)

  • structure in amyloid fibril formation (PMID:11676539)
  • cleaved form partially attains a conformation that has amyloidogenic features (PMID:11801591)
  • solution structure determined by (1)H NMR spectroscopy and restrained modeling calculations (PMID:11847272)
  • Signal transduction of beta2m-induced expression of VCAM-1 and COX-2 in synovial fibroblasts. (PMID:11849381)
  • Strong associations were found between B2M serum levels and chromosome 14q32 abnormalities, but not del(13), in multiple myeloma. (PMID:11877296)
  • basis in developing CD8+ T cell antagonists (PMID:11914379)
  • Conformation of beta 2-microglobulin amyloid fibrils analyzed by reduction of the disulfide bond (PMID:11943769)
  • equilibrium denaturation measured by (1)H-(15)N NMR to determine conformational properties of an amyloidogenic intermediate of human beta(2)-microglobulin (beta(2)m) formed at low pH (PMID:11967566)
  • Mapping the core of the beta(2)-microglobulin amyloid fibril by H/D exchange (PMID:11967567)
  • Assembly of the FcRn alpha-chain with beta(2)microglobulin is important for both transport of FcRn from the ER to the cell surface and efficient pH-dependent IgG binding. (PMID:12006623)
  • Functional reconstitution of human FcRn in Madin-Darby canine kidney cells required co-expression (PMID:12023961)
  • Increased expression of beta 2-microglobulin is associated with multiple drug resistance in tumor cells (PMID:12085191)
  • Crystal structure reveals clues to its amyloidogenic properties (PMID:12119416)
  • Results suggest that the reduced mobility of the denatured state is an important factor for the amylodogenic potential of beta2-microglobulin. (PMID:12192077)
  • A dominant negative mutant of this protein blocks the extracellular folding of MHC I heavy chain (PMID:12454016)
  • results suggest that the apparent iron-deficient phenotype elicited by haemochromatosis protein (HFE) is not linked to beta(2)microglobulin insufficiency (PMID:12464008)
  • Beta2-microglobulin aberrations in diffuse large B-cell lymphoma of the testis and the central nervous system. (PMID:12471623)
  • USF1 & USF2 bind to the B2M E box & regulate its transactivation. NF-kappa B subunits p50 & p65 bind to the kappa B box & p65 transactivates beta(2)m. IRFs1, 2,4,& 8 but not PU.1, bind to the Ets/ISRE. IRF1 & IRF3 are strong transactivators of beta(2)m. (PMID:12480693)
  • taken up by synovial fibroblasts and macrophages of patients with osteoarthritis (PMID:12480959)
  • Data suggest that residues 59-71 may be important in the self-association of partially folded beta(2)microglobulin into amyloid fibrils. (PMID:12488093)
  • Block of b2m expression results in complete loss of HLA class I antigen expression on melanoma cells and disease progression (PMID:12516095)
  • high concentrations retards the generation of monocyte-derived dendritic cells, which may involve down-regulation of major histocompatibility complex class I molecules, inactivation of Raf/MEK/ERK cascade and NF-kappaB, and activation of STAT3 (PMID:12531797)
  • a possible marker of renal function in patients with type 2 diabetes mellitus (PMID:12738401)
  • Our analysis suggests that the favored monomer building block for fibril elongation is the conformation of the isolated beta(2)-microglobulin, without the beta-bulge on strand D and without strands A and G participating in the fibril beta-sheet structure (PMID:12818210)
  • atomic force microscopy study of beta-2 microglobulin (PMID:12850147)
  • beta 2-microglobulin N and C-terminal strands have roles in amyloid formation at neutral pH (PMID:12860117)
  • analysis of beta 2-microglobulin amyloid formation with destabilized proteins (PMID:12860118)
  • Some glycosaminoglycans and proteoglycans could enhance deposition of beta2m amyloid fibrils in vivo, possibly by binding directly to the surface of the fibrils and stabilizing the conformation of beta2m in the fibrils (PMID:12911560)
  • mutations in which proline was introduced to each of the beta-strands of B2M affected the amyloidogenic potential of B2M to various degrees, and demonstrated that stability of the amyloid fibrils is a key factor determining the amyloidogenic potential (PMID:12958308)
  • examined the unfolding processes of B2M and two related variants, a DeltaN6 and a Lys57-Asp58 cleavage, by high-temperature molecular dynamics simulations. Conformational changes of variants may relate to polymerization tendencies related to amyloidosis. (PMID:12968074)
  • Causes dialysis-related amyloidosis, by virtue of its retention when renal function fails, its deposition in tissues, its aggregation into fibrils, and its ability to become glycosylated. Review. (PMID:14681859)
  • structure activity relationship; His31–>Tyr human beta2m mutant, a non-natural form of beta2m that is more stable than the wild-type protein, displaying a ten-fold acceleration of the slow phase of folding (PMID:14698299)
  • the internal structures are similar for beta2-microglobulin and amyloid fibril protein (PMID:14699107)
  • B2M serum levels can be used as a marker for early diagnosis of cytomegalovirus infection after kidney transplantation. (PMID:15194307)
  • Results show that a seven-residue segment of human beta2-microglobulin (beta2M), not found in mouse beta2M, is sufficient to convert beta2M to the amyloid state, and that specific residue interactions are crucial to the conversion. (PMID:15249659)
  • beta(2)-microglobulin shows a similar heat capacity change upon amyloid formation to that of the folding to the native globular state, whereas the enthalpy change of the reaction is lower (PMID:15494406)
  • effects of guanidine hydrochloride on the amyloid fibrils of beta2-m reveal a cooperative unfolding transition similar to that of the native state. (PMID:15498554)
  • an unfolded beta(2)m at C-terminal is found in hemodialysis-related amyloidosis (PMID:15610257)
  • There is an optimal concentration of salts required for efficient fibril growth of beta 2-microglobulin, suggesting that counterion interaction is crucial in amyloid formation. (PMID:15667222)
  • Unfolded delta lysine-58-cleaved beta2m, a slightly modified beta 2-microglobulin variant generated by limited proteolysis, may behave as a monomeric amyloidogenic intermediate under physiologic conditions. (PMID:15766269)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriozmp:0000001138ENSDARG00000071168
mus_musculusB2mENSMUSG00000060802
rattus_norvegicusB2mENSRNOG00000017123

Paralogs (13): HLA-DQB1 (ENSG00000179344), HLA-DRB1 (ENSG00000196126), HLA-DQA1 (ENSG00000196735), HLA-DRB5 (ENSG00000198502), HLA-DOA (ENSG00000204252), HLA-DMA (ENSG00000204257), HLA-DRA (ENSG00000204287), HLA-DPB1 (ENSG00000223865), HLA-DPA1 (ENSG00000231389), HLA-DQB2 (ENSG00000232629), HLA-DQA2 (ENSG00000237541), HLA-DOB (ENSG00000241106), HLA-DMB (ENSG00000242574)

Protein

Protein identifiers

Beta-2-microglobulinP61769 (reviewed: P61769)

All UniProt accessions (4): P61769, H0YLF3, J3KNU0, Q16446

UniProt curated annotations — full annotation on UniProt →

Function. Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system. Exogenously applied M.tuberculosis EsxA or EsxA-EsxB (or EsxA expressed in host) binds B2M and decreases its export to the cell surface (total protein levels do not change), probably leading to defects in class I antigen presentation.

Subunit / interactions. Heterodimer of an alpha chain and a beta chain. Beta-2-microglobulin is the beta-chain of major histocompatibility complex class I molecules. Polymers of beta 2-microglobulin can be found in tissues from patients on long-term hemodialysis. B2M alone (not in complex with HLA-I) interacts with M.tuberculosis EsxA (ESAT-6) and an EsxA-EsxB (CFP-10) complex; the tripartite complex can be detected in the host endoplasmic reticulum. The B2M-EsxA complex can be detected in patients with pleural tuberculosis and is stable from pH 4.0 to 8.0 and in the presence of 2M NaCl. Forms a heterotrimer with HLA-E and a self- or a foreign peptide. Forms a heterotrimer with HLA-G and a self-peptide. Forms a heterotrimer with HLA-F and a self-peptide. Forms a heterotrimer with MR1 and a metabolite antigen.

Subcellular location. Secreted. Cell surface.

Post-translational modifications. Glycation of Ile-21 is observed in long-term hemodialysis patients.

Disease relevance. Immunodeficiency 43 (IMD43) [MIM:241600] A disorder characterized by marked reduction in serum concentrations of immunoglobulins and albumin, and hypoproteinemia due to hypercatabolism. Patients may suffer from recurrent respiratory tract infections and severe skin disease. The disease is caused by variants affecting the gene represented in this entry. Amyloidosis, hereditary systemic 6 (AMYLD6) [MIM:620659] A form of hereditary systemic amyloidosis, a disorder characterized by amyloid deposition in multiple tissues resulting in a wide clinical spectrum. AMYLD6 is mainly characterized by gastrointestinal and cardiac symptoms. Neurologic involvement, sicca syndrome, and carpal tunnel syndrome may also be present. Inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry. Apart from the presence of causative mutations, beta-2-microglobulin may adopt the fibrillar configuration of amyloid, resulting in amyloidosis, when its serum levels are persistently high, as seen in patients on long-term hemodialysis. In contrast to patients with dialysis-related amyloidosis, patients with hereditary amyloidosis have normal circulating concentrations of beta2-microglobulin.

Similarity. Belongs to the beta-2-microglobulin family.

RefSeq proteins (1): NP_004039* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003006Ig/MHC_CSConserved_site
IPR003597Ig_C1-setDomain
IPR007110Ig-like_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR015707B2MicroglobulinFamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050160MHC/ImmunoglobulinFamily

Pfam: PF07654

UniProt features (36 total): strand 12, glycosylation site 7, mutagenesis site 3, sequence conflict 3, chain 2, sequence variant 2, turn 2, signal peptide 1, disulfide bond 1, helix 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

1226 structures, top 30 by resolution.

PDBMethodResolution (Å)
4E0KX-RAY DIFFRACTION0.97
1K5NX-RAY DIFFRACTION1.09
3MREX-RAY DIFFRACTION1.1
2YXFX-RAY DIFFRACTION1.13
8E2ZX-RAY DIFFRACTION1.13
7NMRX-RAY DIFFRACTION1.15
8ROPX-RAY DIFFRACTION1.15
7R7WX-RAY DIFFRACTION1.17
4U1MX-RAY DIFFRACTION1.18
3CZFX-RAY DIFFRACTION1.2
6Y26X-RAY DIFFRACTION1.2
7NMCX-RAY DIFFRACTION1.2
7NMOX-RAY DIFFRACTION1.2
7NMTX-RAY DIFFRACTION1.2
6MT3X-RAY DIFFRACTION1.21
8EC5X-RAY DIFFRACTION1.22
4RMTX-RAY DIFFRACTION1.24
7NN5X-RAY DIFFRACTION1.24
3IB4X-RAY DIFFRACTION1.25
6Y2AX-RAY DIFFRACTION1.25
7NMYX-RAY DIFFRACTION1.25
7TUCX-RAY DIFFRACTION1.25
6V2OX-RAY DIFFRACTION1.27
6Y29X-RAY DIFFRACTION1.28
7WJ2X-RAY DIFFRACTION1.28
3LN4X-RAY DIFFRACTION1.3
3BWAX-RAY DIFFRACTION1.3
3D25X-RAY DIFFRACTION1.3
3MRGX-RAY DIFFRACTION1.3
3SPVX-RAY DIFFRACTION1.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P61769-F194.430.85

Antibody-complex structures (SAbDab): 441W72, 2X89, 3GJF, 3HAE, 4KDT, 4WUU, 5WHK, 6FGB, 6ID4, 6NHA, 6UJ9, 6V7Y, 6V7Z, 6V80, 6W51, 7BBG, 7BH8, 7RE7, 7STF, 7T0L, 7TR4, 8EB2, 8EK5, 8FJA, 8FJB (+19 more)

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): 22

Disulfide bonds (1): 45–100

Glycosylation sites (7): 111, 114, 21, 39, 61, 68, 78

Mutagenesis-validated functional residues (3):

PositionPhenotype
79increases tendency towards amyloid formation.
80decreases tendency towards amyloid formation.
80increases tendency towards amyloid formation.

Function

Pathways and Gene Ontology

Reactome pathways

32 pathways

IDPathway
R-HSA-1236974ER-Phagosome pathway
R-HSA-1236977Endosomal/Vacuolar pathway
R-HSA-164940Nef mediated downregulation of MHC class I complex cell surface expression
R-HSA-198933Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-2172127DAP12 interactions
R-HSA-2424491DAP12 signaling
R-HSA-6798695Neutrophil degranulation
R-HSA-877300Interferon gamma signaling
R-HSA-9637628Modulation by Mtb of host immune system
R-HSA-9705671SARS-CoV-2 activates/modulates innate and adaptive immune responses
R-HSA-977225Amyloid fiber formation
R-HSA-983170Antigen Presentation: Folding, assembly and peptide loading of class I MHC
R-HSA-1236975Antigen processing-Cross presentation
R-HSA-1280215Cytokine Signaling in Immune system
R-HSA-1280218Adaptive Immune System
R-HSA-162906HIV Infection
R-HSA-162909Host Interactions of HIV factors
R-HSA-1643685Disease
R-HSA-164938Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
R-HSA-164952The role of Nef in HIV-1 replication and disease pathogenesis
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-392499Metabolism of proteins
R-HSA-5663205Infectious disease
R-HSA-913531Interferon Signaling
R-HSA-9635486Infection with Mycobacterium tuberculosis
R-HSA-9679506SARS-CoV Infections
R-HSA-9694516SARS-CoV-2 Infection
R-HSA-9705683SARS-CoV-2-host interactions
R-HSA-9824439Bacterial Infection Pathways

MSigDB gene sets: 767 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GSE45365_NK_CELL_VS_CD8A_DC_UP, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_CELL_PROLIFERATION, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_MEMBRANE_DEPOLARIZATION, SHEPARD_BMYB_MORPHOLINO_UP, FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_OR_POLYSACCHARIDE_ANTIGEN_VIA_MHC_CLASS_II, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_NEGATIVE_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, GOBP_COGNITION, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS

GO Biological Process (38): T cell mediated cytotoxicity (GO:0001913), positive regulation of T cell mediated cytotoxicity (GO:0001916), response to molecule of bacterial origin (GO:0002237), antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481), peptide antigen assembly with MHC class I protein complex (GO:0002502), peptide antigen assembly with MHC class II protein complex (GO:0002503), positive regulation of T cell cytokine production (GO:0002726), intracellular iron ion homeostasis (GO:0006879), sensory perception of smell (GO:0007608), learning or memory (GO:0007611), negative regulation of neuron projection development (GO:0010977), antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885), antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886), T cell differentiation in thymus (GO:0033077), transferrin transport (GO:0033572), regulation of iron ion transport (GO:0034756), negative regulation of iron ion transport (GO:0034757), protein refolding (GO:0042026), regulation of erythrocyte differentiation (GO:0045646), positive regulation of receptor-mediated endocytosis (GO:0048260), negative regulation of receptor-mediated endocytosis (GO:0048261), negative regulation of epithelial cell proliferation (GO:0050680), negative regulation of neurogenesis (GO:0050768), positive regulation of immune response (GO:0050778), positive regulation of T cell activation (GO:0050870), protein homotetramerization (GO:0051289), multicellular organismal-level iron ion homeostasis (GO:0060586), cellular response to iron ion (GO:0071281), cellular response to iron(III) ion (GO:0071283), cellular response to nicotine (GO:0071316), amyloid fibril formation (GO:1990000), positive regulation of cellular senescence (GO:2000774), negative regulation of forebrain neuron differentiation (GO:2000978), immune system process (GO:0002376), antigen processing and presentation of peptide antigen via MHC class I (GO:0002474), iron ion transport (GO:0006826), immune response (GO:0006955), response to metal ion (GO:0010038)

GO Molecular Function (6): structural molecule activity (GO:0005198), MHC class II protein complex binding (GO:0023026), peptide antigen binding (GO:0042605), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (26): Golgi membrane (GO:0000139), extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), lysosomal membrane (GO:0005765), endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), focal adhesion (GO:0005925), external side of plasma membrane (GO:0009897), ER to Golgi transport vesicle membrane (GO:0012507), membrane (GO:0016020), phagocytic vesicle membrane (GO:0030670), early endosome membrane (GO:0031901), late endosome membrane (GO:0031902), early endosome lumen (GO:0031905), specific granule lumen (GO:0035580), MHC class I protein complex (GO:0042612), MHC class II protein complex (GO:0042613), MHC class I peptide loading complex (GO:0042824), recycling endosome membrane (GO:0055038), extracellular exosome (GO:0070062), tertiary granule lumen (GO:1904724), HFE-transferrin receptor complex (GO:1990712), cell surface (GO:0009986)

Reactome top-level categories

Rollup of top-15 pathways:

CategoryPathways
Antigen processing-Cross presentation2
Innate Immune System2
Class I MHC mediated antigen processing & presentation2
Immune System2
Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters1
Adaptive Immune System1
DAP12 interactions1
Interferon Signaling1
Infection with Mycobacterium tuberculosis1
SARS-CoV-2-host interactions1
Metabolism of proteins1
Viral Infection Pathways1
HIV Infection1
The role of Nef in HIV-1 replication and disease pathogenesis1
Host Interactions of HIV factors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
iron ion transport3
cellular anatomical structure3
cytoplasm3
positive regulation of T cell mediated immunity2
antigen processing and presentation of peptide antigen via MHC class I2
peptide antigen assembly with MHC protein complex2
antigen processing and presentation of peptide antigen via MHC class II2
endomembrane system2
intracellular membrane-bounded organelle2
early endosome2
endosome membrane2
MHC protein complex2
leukocyte mediated cytotoxicity1
T cell mediated immunity1
positive regulation of leukocyte mediated cytotoxicity1
T cell mediated cytotoxicity1
regulation of T cell mediated cytotoxicity1
response to bacterium1
response to external biotic stimulus1
antigen processing and presentation of exogenous peptide antigen via MHC class Ib1
MHC class I protein complex assembly1
MHC class II protein complex assembly1
T cell cytokine production1
positive regulation of cytokine production involved in immune response1
regulation of T cell cytokine production1
intracellular monoatomic cation homeostasis1
inorganic ion homeostasis1
sensory perception of chemical stimulus1
behavior1
cognition1
regulation of neuron projection development1
neuron projection development1
negative regulation of cell projection organization1
antigen processing and presentation of endogenous peptide antigen1
antigen processing and presentation of exogenous peptide antigen1
T cell differentiation1
protein transport1
regulation of metal ion transport1
regulation of iron ion transport1
negative regulation of monoatomic ion transport1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

269 interactions, top by confidence:

ABTypeScore
B2MB2Mpsi-mi:“MI:0407”(direct interaction)0.980
B2MB2Mpsi-mi:“MI:0195”(covalent binding)0.980
HLA-BB2Mpsi-mi:“MI:0915”(physical association)0.930

BioGRID (146): B2M (Reconstituted Complex), B2M (Affinity Capture-MS), B2M (Affinity Capture-MS), B2M (Affinity Capture-MS), B2M (Affinity Capture-MS), B2M (Affinity Capture-MS), B2M (Synthetic Growth Defect), B2M (Two-hybrid), B2M (Co-localization), B2M (Affinity Capture-MS), RGPD2 (Affinity Capture-MS), FCGRT (Affinity Capture-MS), RGPD5 (Affinity Capture-MS), DLGAP5 (Affinity Capture-MS), TPST1 (Affinity Capture-MS)

ESM2 similar proteins: O42197, O77517, O77518, O77519, O77520, O77521, O77523, O77524, O77525, O77526, O77528, O77529, O77530, O77531, O77533, O77534, O77535, O77536, O77537, P07151, P16213, P55076, P55079, P61769, P61770, P61771, P63060, P63061, P63062, P63063, P63064, P63065, P63066, P63067, P63068, P63069, P63070, P63071, Q03422, Q04475

Diamond homologs: O42197, O77517, O77518, O77519, O77520, O77521, O77523, O77524, O77525, O77526, O77528, O77529, O77530, O77531, O77532, O77533, O77534, O77535, O77536, O77537, P01844, P01885, P01886, P01887, P01888, P01906, P01910, P04227, P04228, P04440, P07151, P14434, P14435, P14436, P14437, P14438, P15981, P16213, P19341, P20036

SIGNOR signaling

5 interactions.

AEffectBMechanism
USF1“up-regulates quantity by expression”B2M“transcriptional regulation”
USF2“up-regulates quantity by expression”B2M“transcriptional regulation”
RELA“up-regulates quantity by expression”B2M“transcriptional regulation”
NfKb-p65/p50“up-regulates quantity by expression”B2M“transcriptional regulation”
B2M“form complex”“Class I MHC”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 77 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Antigen Presentation: Folding, assembly and peptide loading of class I MHC878.8×2e-11
ER-Phagosome pathway825.9×5e-08
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell1124.0×7e-11
Interferon alpha/beta signaling622.8×1e-05
Interferon gamma signaling618.8×4e-05
SARS-CoV-2 activates/modulates innate and adaptive immune responses817.8×9e-07

GO biological processes:

GO termPartnersFoldFDR
positive regulation of T cell mediated cytotoxicity10113.5×2e-16
adaptive immune response815.0×3e-06
immune response1414.6×5e-11

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 7 cancer types — CESC, DLBCLNOS, HNSC, MEL, MLYM, NHL, NSCLC.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic3
Uncertain significance39
Likely benign33
Benign1

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
2824511NM_004048.4(B2M):c.20T>A (p.Leu7Ter)Pathogenic
31907NM_004048.4(B2M):c.286G>A (p.Asp96Asn)Pathogenic
217869NM_004048.4(B2M):c.67+1G>TLikely pathogenic
3577174NM_004048.4(B2M):c.2T>C (p.Met1Thr)Likely pathogenic
4808285NM_004048.4(B2M):c.68-2A>CLikely pathogenic

SpliceAI

402 predictions. Top by Δscore:

VariantEffectΔscore
15:44711612:GC:Gdonor_gain1.0000
15:44711614:G:GGdonor_gain1.0000
15:44715418:CTCA:Cacceptor_loss1.0000
15:44715419:TCA:Tacceptor_loss1.0000
15:44715420:CAG:Cacceptor_loss1.0000
15:44715421:A:ACacceptor_loss1.0000
15:44715641:GA:Gdonor_gain1.0000
15:44715693:T:Gdonor_gain1.0000
15:44715697:GTGGG:Gdonor_gain1.0000
15:44715699:GGG:Gdonor_gain1.0000
15:44715700:GG:Gdonor_gain1.0000
15:44715700:GGG:Gdonor_gain1.0000
15:44715701:GG:Gdonor_gain1.0000
15:44716313:A:AGacceptor_gain1.0000
15:44716313:ACT:Aacceptor_gain1.0000
15:44716314:C:Gacceptor_gain1.0000
15:44716315:T:Aacceptor_gain1.0000
15:44716326:T:Gacceptor_gain1.0000
15:44716327:A:AGacceptor_gain1.0000
15:44716328:G:GGacceptor_gain1.0000
15:44716328:GA:Gacceptor_gain1.0000
15:44716328:GATC:Gacceptor_gain1.0000
15:44716355:AGGT:Adonor_loss1.0000
15:44716356:GGT:Gdonor_loss1.0000
15:44716357:G:Tdonor_loss1.0000
15:44716358:T:Adonor_loss1.0000
15:44717601:TTTCA:Tacceptor_loss1.0000
15:44717602:TTCA:Tacceptor_loss1.0000
15:44717603:TCA:Tacceptor_loss1.0000
15:44717604:CAG:Cacceptor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000219847 (15:44712011 C>T), RS1000272307 (15:44711761 G>A,C), RS1000540082 (15:44717506 T>C), RS1000606334 (15:44710366 A>G), RS1000996352 (15:44711811 C>A,T), RS1001671393 (15:44714931 T>A), RS1001988503 (15:44713070 A>G), RS1001996727 (15:44713468 C>A), RS1002553374 (15:44714300 A>G), RS1002617998 (15:44715854 G>A), RS1002665848 (15:44716125 A>C,G,T), RS1002672364 (15:44716446 G>C,T), RS1004444280 (15:44712535 G>T), RS1004630351 (15:44712734 T>C,G), RS1004777040 (15:44711100 A>G)

Disease associations

OMIM: gene MIM:109700 | disease phenotypes: MIM:241600, MIM:105200, MIM:620659, MIM:604360

GenCC curated gene-disease

DiseaseClassificationInheritance
hypoproteinemia, hypercatabolicStrongAutosomal recessive
variant ABeta2M amyloidosisStrongAutosomal dominant
MHC class I deficiencySupportiveAutosomal recessive
familial visceral amyloidosisLimitedAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
hypoproteinemia, hypercatabolicLimitedAR

Mondo (7): hypoproteinemia, hypercatabolic (MONDO:0009434), familial visceral amyloidosis (MONDO:0007099), amyloidosis, hereditary systemic 6 (MONDO:0971010), non-Hodgkin lymphoma (MONDO:0018908), hereditary spastic paraplegia 11 (MONDO:0011445), variant ABeta2M amyloidosis (MONDO:0017810), MHC class I deficiency (MONDO:0011476)

Orphanet (3): Hereditary amyloidosis with primary renal involvement (Orphanet:85450), Non-Hodgkin lymphoma (Orphanet:547), Autosomal recessive spastic paraplegia type 11 (Orphanet:2822)

HPO phenotypes

51 total (30 of 51 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000157Abnormality of the tongue
HP:0000969Edema
HP:0001271Polyneuropathy
HP:0001278Orthostatic hypotension
HP:0001482Subcutaneous nodule
HP:0001824Weight loss
HP:0001917Renal amyloidosis
HP:0002028Chronic diarrhea
HP:0002094Dyspnea
HP:0002110Bronchiectasis
HP:0002176Spinal cord compression
HP:0002205Recurrent respiratory infections
HP:0002756Pathologic fracture
HP:0002986Radial bowing
HP:0003022Hypoplasia of the ulna
HP:0003073Hypoalbuminemia
HP:0003075Hypoproteinemia
HP:0003365Arthralgia of the hip
HP:0003621Juvenile onset
HP:0004315Decreased circulating IgG concentration
HP:0005244Gastrointestinal infarctions
HP:0007141Sensorimotor neuropathy
HP:0010286Abnormal salivary gland morphology
HP:0010976Decreased total B cell count
HP:0011805Abnormal skeletal muscle morphology
HP:0011915Cardiovascular calcification
HP:0012065Multiple bony cystic lesions
HP:0012185Constrictive median neuropathy

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

DescriptorNameTree numbers
D008228Lymphoma, Non-HodgkinC04.557.386.480; C15.604.515.569.480; C20.683.515.761.480
C538249Amyloidosis, familial visceral (supp.)
C565476Hypoproteinemia, Hypercatabolic (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL1741302 (SINGLE PROTEIN), CHEMBL5465401 (PROTEIN COMPLEX)

Clinical evidence (CIViC)

Drug × variant × indication: 1 predictive associations from 1 curated evidence items.

VariantTherapyIndicationEffectLevelCIViC
B2M S14FSPembrolizumabSkin MelanomaResistanceCIViC CEID1569

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

Binding affinities (BindingDB)

1 measured of 5 human assays (7 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
(4S,4aR,5S,5aS,12aS)-4-(dimethylamino)-5,10,12a-trihydroxy-1,3,11,12-tetraketo-6-methylene-4a,5,5a,11a-tetrahydro-4H-tetracene-2-carboxamide;hydrochlorideIC50122000 nM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation8
Cadmiumaffects secretion, increases expression, increases secretion, increases abundance, affects reaction4
trichostatin Aaffects cotreatment, increases expression3
Air Pollutantsincreases abundance, decreases expression, affects expression3
Arsenicincreases expression, increases abundance, increases secretion, decreases expression3
Metriboloneincreases secretion, decreases reaction, increases expression3
bisphenol Aaffects expression, increases expression2
sodium arsenitedecreases expression, increases abundance2
chloropicrinaffects expression, decreases expression2
Decitabineaffects expression, increases expression2
Acetaminophenincreases expression2
Air Pollutants, Occupationalincreases expression2
Copperaffects binding, decreases folding, decreases stability, increases reaction2
Estradioldecreases expression, increases expression2
Ifosfamideincreases expression2
Leadaffects expression, increases abundance, increases secretion2
Nickelincreases expression2
Ozoneaffects expression, increases abundance, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Rotenonedecreases expression, increases expression2
Smokeincreases abundance, decreases expression2
Dihydrotestosteroneincreases expression, decreases reaction2
Tretinoinincreases expression2
bisphenol Fincreases expression1
shuanghuang shengbaiincreases expression1
napabucasindecreases expression1
dicrotophosdecreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
uranyl acetateaffects expression1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5650979BindingBinding affinity to human B2M incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

205 cell lines: 162 cancer cell line, 17 spontaneously immortalized cell line, 17 induced pluripotent stem cell, 6 embryonic stem cell, 3 transformed cell line

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

CellosaurusNameCategorySex
CVCL_0008DaudiCancer cell lineMale
CVCL_0248DLD-1Cancer cell lineMale
CVCL_0292HCT 15Cancer cell lineMale
CVCL_0399LoVoCancer cell lineMale
CVCL_1514NCI-H2009Cancer cell lineFemale
CVCL_1533NCI-H2135Cancer cell lineSex unspecified
CVCL_1550NCI-H2347Cancer cell lineFemale
CVCL_1616OC 314Cancer cell lineFemale
CVCL_1618OC 316Cancer cell lineFemale
CVCL_1707SNG-MCancer cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00090038PHASE4COMPLETEDEffect of Rituximab on Immunological Recall Response to Specific Antigens in the Treatment of Non-Hodgkin’s Lymphoma
NCT00162955PHASE4COMPLETEDPrevention of CHOP-induced Chronic Cardiotoxicity
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00352703PHASE4COMPLETEDPROMPT - Palifermin in Reduction of Oral Mucositis in PBSC Transplantation
NCT00430352PHASE4COMPLETEDMAXIMA Study: A Study of Maintenance Therapy With MabThera (Rituximab) in Patients With Non-Hodgkin’s Lymphoma.
NCT00797810PHASE4UNKNOWNIntensification Therapy of Mature B-ALL, Burkitt and Burkitt Like and Other High Grade Non-Hodgkin’s Lymphoma in Adults
NCT00808171PHASE4COMPLETEDEvaluation of the Analgesy With Emla and/or Nitrous Oxide in Pediatric Patients for Lumbar Puncture
NCT00926757PHASE4COMPLETEDProphylactic Use of Entecavir for Non-Hodgkin’s Lymphoma Patients With Resolved Hepatitis B
NCT00969462PHASE4COMPLETEDDoxorubicin Pharmacokinetics and Response in Non Hodgkin’s Lymphoma
NCT01124526PHASE4COMPLETEDEfficacy Response Duration and Toxicity of Rituximab, Fludarabine, and Cyclophosphamide (RFC) as 1st Line Treatment and Rituximab (R) in Maintenance Treatment in Follicular Non Hodgkin (FNH) Lymphoma
NCT01164475PHASE4COMPLETEDEvaluation of Approved Weight-Based Dose Compared to Fixed Dose of Plerixafor in Patients With Non-Hodgkin’s Lymphoma (NHL) Weighing Less Than 70 Kilograms
NCT01180049PHASE4COMPLETEDComparison Of 2 Doses Of Temsirolimus (Torisel) In Patients With Mantle Cell Lymphoma
NCT02782845PHASE4COMPLETEDAn Expanded Access Program of Pegfilgrastim (Neulastim) in Participants With Non-Hodgkin’s Lymphoma (NHL)
NCT05191225PHASE4UNKNOWNUltrafast Truxima Infusion in Non-Hodgkin’s Lymphoma: Txagorapid Study
NCT06665737PHASE4NOT_YET_RECRUITINGOutcomes of Early and Late Administration G-CSF for Primary Prophylaxis in Non-Hodgkin’s Lymphoma Patients
NCT06876649PHASE4RECRUITINGA Master Protocol to Evaluate the Long-Term Safety of (LY3527727) Pirtobrutinib
NCT06876662PHASE4RECRUITINGA Study of (LY3527727) Pirtobrutinib in Participants With Previously Treated Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma or Non-Hodgkin Lymphoma
NCT07016165PHASE4RECRUITINGCiprofloxacin vs Ceftazidime for Empirical Treatment of High-Risk Neutropenic Fever in Children With Hematologic Malignancies
NCT00039910PHASE3COMPLETEDSafety and Efficacy of (PN-152,243)/PN-196,444 in the Prevention of Thrombocytopenia
NCT00057343PHASE3TERMINATEDSafety and Efficacy of Zevalin in the Treatment of Non-Hodgkin’s Lymphoma
NCT00078598PHASE3UNKNOWNA Study of Rituximab Versus Iodine I 131 Tositumomab Therapy for Patients With Non-Hodgkin’s Lymphoma
NCT00091676PHASE3UNKNOWNStudy of the BiovaxId Tumor Derived Idiotype Vaccine in Patients With Follicular Lymphoma
NCT00129090PHASE3COMPLETEDMega-CHOEP: Conventional Chemo Vs HD Chemo Followed by Auto SCT in Younger Pts With Aggressive Non-Hodgkin’s Lymphoma
NCT00133302PHASE3TERMINATEDStudy of Standard CHOP Versus Biweekly CHOP in Aggressive Non-Hodgkin’s Lymphoma (JCOG9809)
NCT00139841PHASE3COMPLETEDSafety and Efficacy of Treanda™ (Bendamustine HCl) in Patients With Indolent Non-Hodgkin’s Lymphoma (NHL) Who Are Refractory to Rituximab
NCT00145652PHASE3COMPLETEDAdjuvant I.V. Iron Therapy During Erythropoetin Treatment of Anemic Patients With Lymphoproliferative Disorders.
NCT00152139PHASE3COMPLETEDStem Cell Transplantation for Patients With Hematologic Malignancies
NCT00269113PHASE3COMPLETEDA Study of MabThera (Rituximab) in Patients With Advanced Non-Hodgkin’s Lymphoma
NCT00312845PHASE3COMPLETEDStudy of VELCADE and Rituximab in Patients With Relapsed or Refractory B-cell Non-Hodgkin’s Lymphoma
NCT00332202PHASE3COMPLETEDPRELUDE:Study to Investigate the Prevention of Relapse in Lymphoma Using Daily Enzastaurin
NCT00352846PHASE3COMPLETEDEffect of Zoledronic Acid on Chemotherapy Induced Bone Loss
NCT00398411PHASE3COMPLETEDMoxifloxacin in the Prevention of Bacteremia After High-dose Chemotherapy and Transplantation of Peripheral Stem Cells
NCT00463463PHASE3UNKNOWNZevalin and BEAM High-dose Chemotherapy Compared With BEAM Alone as Conditioning Regimen in Patients With Chemosensitive Relapse of Non-Hodgkin’s Lymphoma
NCT00491491PHASE3COMPLETEDZevalin-beam for Aggressive Lymphoma
NCT00577161PHASE3WITHDRAWNFludarabine, Pixantrone and Rituximab vs Fludarabine and Rituximab forRelapsed or Refractory Indolent NHL
NCT00719472PHASE3COMPLETEDA Study of Rituximab Alternative Dosing Rate in Patients With Previously Untreated Diffuse Large B-cell or Follicular Non-Hodgkin’s Lymphoma (RATE)
NCT00877006PHASE3COMPLETEDStudy of Bendamustine Hydrochloride and Rituximab (BR) Compared With R-CVP or R-CHOP in the First-Line Treatment of Patients With Advanced Indolent Non-Hodgkin’s Lymphoma (NHL) or Mantle Cell Lymphoma (MCL) - Referred to as the BRIGHT Study
NCT00877214PHASE3ACTIVE_NOT_RECRUITINGSignificance of Duration of Maintenance Therapy With Rituximab in Non-Hodgkin Lymphomas
NCT00928018PHASE3COMPLETEDTacrolimus/Sirolimus/Methotrexate vs Tacrolimus/Methotrexate or Cyclosporine/Mycophenolate Mofetil for GVHD Prophylaxis After Reduced Intensity Allogeneic Stem Cell Transplantation for Patients With Lymphoma
NCT00991211PHASE3COMPLETEDBendamustine Plus Rituximab Versus CHOP Plus Rituximab