SIRPB1

gene
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Also known as SIRP-BETA-1CD172bSIRB1

Summary

SIRPB1 (signal regulatory protein beta 1, HGNC:15928) is a protein-coding gene on chromosome 20p13, encoding Signal-regulatory protein beta-1 (O00241). Immunoglobulin-like cell surface receptor involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes.

The protein encoded by this gene is a member of the signal-regulatory-protein (SIRP) family, and also belongs to the immunoglobulin superfamily. SIRP family members are receptor-type transmembrane glycoproteins known to be involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. This protein was found to interact with TYROBP/DAP12, a protein bearing immunoreceptor tyrosine-based activation motifs. This protein was also reported to participate in the recruitment of tyrosine kinase SYK. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10326 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 82 total
  • MANE Select transcript: NM_006065

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15928
Approved symbolSIRPB1
Namesignal regulatory protein beta 1
Location20p13
Locus typegene with protein product
StatusApproved
AliasesSIRP-BETA-1, CD172b, SIRB1
Ensembl geneENSG00000101307
Ensembl biotypeprotein_coding
OMIM603889
Entrez10326

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 17 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000262929, ENST00000279477, ENST00000381596, ENST00000381603, ENST00000381605, ENST00000562014, ENST00000563840, ENST00000565076, ENST00000565087, ENST00000565230, ENST00000565775, ENST00000566055, ENST00000568365, ENST00000569387, ENST00000569629, ENST00000876186, ENST00000876187, ENST00000969009, ENST00000969010, ENST00000969011

RefSeq mRNA: 5 — MANE Select: NM_006065 NM_001083910, NM_001135844, NM_001329157, NM_001330639, NM_006065

CCDS: CCDS13019, CCDS42850, CCDS46571, CCDS82591

Canonical transcript exons

ENST00000381605 — 6 exons

ExonStartEnd
ENSE0000116569115661531566267
ENSE0000160328915717201572037
ENSE0000179247415708051571137
ENSE0000195871015613851565497
ENSE0000357333415783381578694
ENSE0000389976616198691620009

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 97.71.

FANTOM5 (CAGE): breadth broad, TPM avg 13.9686 / max 2498.3457, expressed in 436 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
18604110.9682361
1860382.2259175
1860400.6545177
1860390.119950

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057697.71gold quality
mononuclear cellCL:000084296.82gold quality
leukocyteCL:000073896.78gold quality
granulocyteCL:000009494.21gold quality
bloodUBERON:000017893.72gold quality
right lungUBERON:000216788.92gold quality
spleenUBERON:000210685.78gold quality
bone marrowUBERON:000237185.36gold quality
bone marrow cellCL:000209284.82gold quality
vermiform appendixUBERON:000115483.75gold quality
gall bladderUBERON:000211083.21gold quality
tongue squamous epitheliumUBERON:000691982.20gold quality
caecumUBERON:000115381.71gold quality
diaphragmUBERON:000110380.19gold quality
lymph nodeUBERON:000002979.84gold quality
upper lobe of left lungUBERON:000895279.19gold quality
buccal mucosa cellCL:000233678.43gold quality
upper lobe of lungUBERON:000894878.18gold quality
spermCL:000001977.28gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.83gold quality
male germ cellCL:000001576.56gold quality
mucosa of paranasal sinusUBERON:000503073.85gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099173.14gold quality
gingival epitheliumUBERON:000194972.80gold quality
olfactory bulbUBERON:000226471.39gold quality
CA1 field of hippocampusUBERON:000388171.39gold quality
prefrontal cortexUBERON:000045171.29gold quality
left ventricle myocardiumUBERON:000656671.23gold quality
hair follicleUBERON:000207370.69gold quality
cardiac muscle of right atriumUBERON:000337969.86gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-6678yes25.55
E-ANND-3yes12.33
E-MTAB-9801yes6.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting SIRPB1, 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-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-4425100.0067.591049
HSA-MIR-12118100.0065.881270
HSA-MIR-6127100.0066.762188
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-153-5P99.8973.866317
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-427199.8868.322244
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-453099.6966.471509
HSA-MIR-182799.6368.573265
HSA-MIR-3616-5P99.5567.02989
HSA-MIR-57399.5567.44955

Literature-anchored findings (GeneRIF, showing 9)

  • SIRP beta 1 is a disulfide-linked homodimer in leukocytes that regulates neutrophil transepithelial migration (PMID:16081415)
  • This protein has been found differentially expressed in the temporal lobe from patients with schizophrenia. (PMID:19034380)
  • Using shotgun mass spectrometry, we found this protein differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia. (PMID:19165527)
  • SIRPbeta1 is a novel IFN-induced microglial receptor that supports clearance of neural debris and Abeta aggregates by stimulating phagocytosis. (PMID:19893026)
  • A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)
  • SIRPB1 copy-number polymorphism was significantly associated with impulsive-disinhibited personality scores in a dose-dependent manner. (PMID:25039969)
  • Deletions in Genes Participating in Innate Immune Response Modify the Clinical Course of Andes Orthohantavirus Infection. (PMID:31349540)
  • An Insertion Within SIRPbeta1 Shows a Dual Effect Over Alzheimer’s Disease Cognitive Decline Altering the Microglial Response. (PMID:38427484)
  • SIRPB1 regulates inflammatory factor expression in the glioma microenvironment via SYK: functional and bioinformatics insights. (PMID:38594692)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
mus_musculusSirpaENSMUSG00000037902
mus_musculusSirpb1cENSMUSG00000074677
mus_musculusGm5150ENSMUSG00000078780
mus_musculusSirpdENSMUSG00000078783
mus_musculusSirpb1bENSMUSG00000095028
mus_musculusSirpb1aENSMUSG00000095788
rattus_norvegicusSirpaENSRNOG00000004763
rattus_norvegicusLOC100909964ENSRNOG00000043478
rattus_norvegicusAABR07008876.1ENSRNOG00000053292

Paralogs (4): SIRPG (ENSG00000089012), SIRPD (ENSG00000125900), SIRPB2 (ENSG00000196209), SIRPA (ENSG00000198053)

Protein

Protein identifiers

Signal-regulatory protein beta-1O00241 (reviewed: O00241, Q5TFQ8)

Alternative names: CD172 antigen-like family member B

All UniProt accessions (9): O00241, Q5TFQ8, H3BQ21, H3BRP9, H3BSK5, H3BTT9, H3BU43, H3BUW0, H9KV29

UniProt curated annotations — full annotation on UniProt →

Function. Immunoglobulin-like cell surface receptor involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. Also participates in the recruitment of tyrosine kinase SYK. Triggers activation of myeloid cells when associated with TYROBP.

Subunit / interactions. Homodimer; disulfide-linked. Interacts with TYROBP. This interaction results in the recruitment of SYK.

Subcellular location. Cell membrane.

Tissue specificity. Detected in monocytes and dendritic cells.

Post-translational modifications. N-glycosylated.

Isoforms (3)

UniProt IDNamesCanonical?
O00241-11yes
O00241-22
Q5TFQ8-13

RefSeq proteins (5): NP_001077379, NP_001129316, NP_001316086, NP_001317568, NP_006056* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003597Ig_C1-setDomain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR051755Ig-like_CS_ReceptorFamily

Pfam: PF07654, PF07686

UniProt features (65 total): strand 24, glycosylation site 6, disulfide bond 6, sequence variant 6, domain 6, topological domain 4, signal peptide 2, chain 2, sequence conflict 2, helix 2, transmembrane region 2, splice variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
2JJUX-RAY DIFFRACTION1.19
2JJVX-RAY DIFFRACTION1.8
2D9CSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00241-F184.760.66
AF-Q5TFQ8-F185.610.67

Functional residue map

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

O00241 (canonical)

Disulfide bonds (3): 54–120, 169–227, 320

Glycosylation sites (3): 291, 244, 269

Q5TFQ8

Disulfide bonds (3): 54–120, 169–227, 272–330

Glycosylation sites (3): 244, 291, 318

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-2172127DAP12 interactions
R-HSA-391160Signal regulatory protein family interactions
R-HSA-6798695Neutrophil degranulation
R-HSA-1500931Cell-Cell communication
R-HSA-168249Innate Immune System
R-HSA-168256Immune System

MSigDB gene sets: 158 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_REGULATION_OF_CELL_ACTIVATION, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, GOCC_SECRETORY_GRANULE, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GCM_PRKCG, GOBP_CELL_CELL_ADHESION, GCM_RING1, GCM_FCGR2B, OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN, GOBP_POSITIVE_REGULATION_OF_CELL_ACTIVATION

GO Biological Process (4): signal transduction (GO:0007165), cell surface receptor signaling pathway (GO:0007166), positive regulation of phagocytosis (GO:0050766), positive regulation of T cell activation (GO:0050870)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): plasma membrane (GO:0005886), cell surface (GO:0009986), secretory granule membrane (GO:0030667), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Innate Immune System2
Cell-Cell communication1
Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
signal transduction1
phagocytosis1
positive regulation of endocytosis1
regulation of phagocytosis1
T cell activation1
regulation of T cell activation1
positive regulation of lymphocyte activation1
positive regulation of leukocyte cell-cell adhesion1
binding1
membrane1
cell periphery1
secretory granule1
cytoplasmic vesicle membrane1
bounding membrane of organelle1

Protein interactions and networks

STRING

1123 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SIRPB1TYROBPO43914990
SIRPB1CD47Q08722905
SIRPB1FCER1GP30273732
SIRPB1PTPN11Q06124707
SIRPB1TREM2Q9NZC2690
SIRPB1OSCARQ8IYS5581
SIRPB1TREM1Q9NP99508
SIRPB1CD200R1Q8TD46463
SIRPB1CLEC5AQ9NY25446
SIRPB1TMEM86BQ8N661411
SIRPB1SIRPAP78324407
SIRPB1ZNF654Q8IZM8397
SIRPB1TMEM265A0A087WTH1390
SIRPB1PTGR3Q8N4Q0389
SIRPB1IGLL1P15814381

IntAct

10 interactions, top by confidence:

ABTypeScore
TYROBPSIRPB1psi-mi:“MI:0915”(physical association)0.520
SIRPB1TYROBPpsi-mi:“MI:0915”(physical association)0.520
SIRPB1CD47psi-mi:“MI:0407”(direct interaction)0.440
SIRPB1Sykpsi-mi:“MI:0915”(physical association)0.400
SIRPB1PTPRFpsi-mi:“MI:0915”(physical association)0.400
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
SIRPASIRPB1psi-mi:“MI:0914”(association)0.350

BioGRID (15): SIRPB1 (Two-hybrid), SIRPB1 (Two-hybrid), RBPMS (Two-hybrid), SIRPB1 (Two-hybrid), APOC1 (Two-hybrid), BPIFA1 (Two-hybrid), SIRPB1 (Affinity Capture-MS), TYROBP (Affinity Capture-Western), SIRPB1 (Affinity Capture-Western), TYROBP (Affinity Capture-Western), SYK (Affinity Capture-Western), SIRPB1 (Affinity Capture-MS), SIRPB1 (Affinity Capture-MS), SIRPB1 (Cross-Linking-MS (XL-MS)), SIRPA (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0R4IGV4, A0A8M2B818, A0JM41, A2VD98, B0CLX4, B6ZK77, D3YX43, F1LW30, O00241, O18906, O54901, O88775, O95256, P00545, P04218, P0C673, P10522, P13369, P17948, P21995, P27931, P35916, P35917, P35969, P37301, P42071, P42703, P53767, Q08DK1, Q15762, Q58EG3, Q5DX21, Q5FWR8, Q5R412, Q5U2P2, Q5VJ70, Q6GMZ9, Q6PCB8, Q6X936, Q7TSN7

Diamond homologs: O00241, O46631, P01691, P01844, P01845, P01847, P01915, P04230, P04231, P18211, P18468, P18469, P18470, P20040, P78324, P97710, P97797, Q5JXA9, Q5TFQ8, Q9H106, Q9P1W8, Q9PWR4, P55899, Q29980, A0A5B9, A0M8Q6, B9A064, O42197, P01834, P01835, P01836, P01837, P01838, P01839, P01840, P01841, P01843, P01846, P01850, P01854

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign10
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2166 predictions. Top by Δscore:

VariantEffectΔscore
20:1598820:A:ACdonor_gain1.0000
20:1598821:C:CCdonor_gain1.0000
20:1598821:CAGT:Cdonor_gain1.0000
20:1611356:CCA:Cdonor_gain1.0000
20:1611356:CCACG:Cdonor_gain1.0000
20:1578329:TGTAC:Tdonor_loss0.9900
20:1578330:GTACT:Gdonor_loss0.9900
20:1578331:TACT:Tdonor_loss0.9900
20:1578332:AC:Adonor_loss0.9900
20:1578333:CT:Cdonor_loss0.9900
20:1578334:TCACC:Tdonor_loss0.9900
20:1578335:CACCG:Cdonor_loss0.9900
20:1578337:C:CTdonor_loss0.9900
20:1578337:CCGCG:Cdonor_gain0.9900
20:1598821:CA:Cdonor_gain0.9900
20:1611348:TGTAC:Tdonor_loss0.9900
20:1611349:GTACT:Gdonor_loss0.9900
20:1611350:TACT:Tdonor_loss0.9900
20:1611351:AC:Adonor_loss0.9900
20:1611352:CT:Cdonor_loss0.9900
20:1611353:TCACC:Tdonor_loss0.9900
20:1611354:CACCA:Cdonor_loss0.9900
20:1611355:A:ACdonor_gain0.9900
20:1611355:A:AGdonor_loss0.9900
20:1611356:C:CCdonor_gain0.9900
20:1611711:CCC:Cacceptor_gain0.9900
20:1611712:CC:Cacceptor_gain0.9900
20:1611712:CCC:Cacceptor_gain0.9900
20:1611713:CC:Cacceptor_gain0.9900
20:1611713:CCT:Cacceptor_loss0.9900

AlphaMissense

2572 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:1571949:G:CF174L0.979
20:1571949:G:TF174L0.979
20:1571951:A:GF174L0.979
20:1578570:C:AW67C0.976
20:1578570:C:GW67C0.976
20:1578572:A:GW67R0.972
20:1578572:A:TW67R0.972
20:1578412:C:GC120S0.970
20:1578413:A:TC120S0.970
20:1571058:G:CF277L0.969
20:1571058:G:TF277L0.969
20:1571060:A:GF277L0.969
20:1571924:A:GW183R0.969
20:1571924:A:TW183R0.969
20:1578610:C:GC54S0.969
20:1578611:A:TC54S0.969
20:1578419:A:CY118D0.965
20:1578411:A:CC120W0.957
20:1578412:C:TC120Y0.954
20:1578402:G:CF123L0.953
20:1578402:G:TF123L0.953
20:1578404:A:GF123L0.953
20:1578413:A:GC120R0.953
20:1571074:C:GC272S0.949
20:1571075:A:TC272S0.949
20:1578611:A:GC54R0.946
20:1571033:A:GW286R0.945
20:1571033:A:TW286R0.945
20:1571922:C:AW183C0.944
20:1571922:C:GW183C0.944

dbSNP variants (sampled 300 via entrez): RS1000311208 (20:1618283 T>C), RS1000372415 (20:1617448 C>A), RS1000479513 (20:1571663 A>G), RS1000592171 (20:1567076 T>A), RS1000743664 (20:1617198 C>T), RS1000907907 (20:1586637 C>G), RS1000930883 (20:1562111 C>T), RS1000987890 (20:1608425 C>T), RS1001007838 (20:1562453 C>A,G), RS1001158200 (20:1573109 C>T), RS1001170886 (20:1594861 T>G), RS1001236876 (20:1585304 A>G), RS1001290780 (20:1608702 G>A), RS1001339778 (20:1563812 T>A,C), RS1001515090 (20:1562614 T>C)

Disease associations

OMIM: gene MIM:603889 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST004599_203Mean platelet volume3.000000e-41
GCST006585_87Blood protein levels5.000000e-226
GCST009391_950Metabolite levels3.000000e-06
GCST011096_27Systemic lupus erythematosus3.000000e-08
GCST90002389_412Lymphocyte percentage of white cells9.000000e-10
GCST90002393_676Monocyte count4.000000e-17
GCST90002395_582Mean platelet volume3.000000e-100
GCST90002398_95Neutrophil count1.000000e-10
GCST90002400_103Plateletcrit5.000000e-30
GCST90002401_303Platelet distribution width9.000000e-21
GCST90002407_637White blood cell count6.000000e-10

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0010403triacylglycerol 48:0 measurement
EFO:0007993lymphocyte percentage of leukocytes
EFO:0005091monocyte count
EFO:0004833neutrophil count
EFO:0007985platelet crit
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Estradiolaffects cotreatment, decreases expression, increases expression2
triphenyl phosphateaffects expression1
arseniteaffects binding, decreases reaction1
mono-(2-ethylhexyl)phthalatedecreases expression1
zinc chromateincreases abundance, increases expression1
benzo(e)pyrenedecreases methylation1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
clothianidinincreases expression1
NSC 689534increases expression1
Rosiglitazoneincreases expression1
Zoledronic Acidincreases expression1
Norethindrone Acetateaffects cotreatment, increases expression1
Allergensdecreases expression1
Azacitidinedecreases expression1
Benzo(a)pyreneaffects methylation1
Bucladesineaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Methapyrilenedecreases methylation1
Methotrexateincreases expression1
Methyl Methanesulfonatedecreases expression1
Nickelincreases expression1
Smokeincreases expression1
Testosteronedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Triclosandecreases expression1
Vincristinedecreases expression1
Aflatoxin B1decreases methylation1

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.