SIRPB1

signal regulatory protein beta 1, the group of Signal regulatory proteins|V-set domain containing|CD molecules|C1-set domain containing

Basic information

Region (hg38): 20:1561385-1620061

Links

ENSG00000101307NCBI:10326OMIM:603889HGNC:15928Uniprot:O00241, Q5TFQ8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIRPB1 gene.

  • not_specified (59 variants)
  • not_provided (2 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIRPB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006065.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
missense
52
clinvar
7
clinvar
59
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 52 10 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SIRPB1protein_codingprotein_codingENST00000381605 556541
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.31e-120.018912558201661257480.000660
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5822552301.110.00001372547
Missense in Polyphen4548.1170.93522625
Synonymous-2.1312194.61.280.00000580847
Loss of Function-0.3571715.51.107.51e-7172

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001140.00114
Ashkenazi Jewish0.0002990.000298
East Asian0.003060.00305
Finnish0.00004670.0000462
European (Non-Finnish)0.0001940.000193
Middle Eastern0.003060.00305
South Asian0.001800.00180
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Immunoglobulin-like cell surface receptor involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. Participates also in the recruitment of tyrosine kinase SYK.;
Pathway
Osteoclast differentiation - Homo sapiens (human);Neutrophil degranulation;DAP12 interactions;Innate Immune System;Immune System;Signal regulatory protein family interactions;Cell-Cell communication (Consensus)

Recessive Scores

pRec
0.0943

Intolerance Scores

loftool
0.970
rvis_EVS
3.22
rvis_percentile_EVS
99.36

Haploinsufficiency Scores

pHI
0.0960
hipred
N
hipred_score
0.133
ghis
0.399

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.458

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sirpb1c
Phenotype

Gene ontology

Biological process
signal transduction;cell surface receptor signaling pathway;positive regulation of cell-cell adhesion;neutrophil degranulation;innate immune response;positive regulation of phagocytosis;positive regulation of T cell activation
Cellular component
plasma membrane;integral component of plasma membrane;cell surface;secretory granule membrane
Molecular function
protein binding