SIRPB1

protein-coding

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

Gene summary

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. [provided by RefSeq, Feb 2009]

MANE transcript

NM_006065.5

Inheritance

—

ClinVar variants

U:64B:10

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr20:1,561,385-1,620,061

External References & Databases

Ensembl (ENSG00000101307)

UniProt (O00241, Q5TFQ8)

Transcript & Mutation Effects

hg38 • Region Span ~58.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SIRPB1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006065.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar		4
missense			62 clinvar	7 clinvar		69
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	10	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006065.5	RefSeq	NP_006056.2	5	MANE Select
ENST00000381605.9	Ensembl	ENSP00000371018.5	5	MANE Select
NM_001083910.4	RefSeq	NP_001077379.1	3	Standard
NM_001135844.4	RefSeq	NP_001129316.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Osteoclast differentiation - Homo sapiens (human)
Neutrophil degranulation
DAP12 interactions
Innate Immune System
Immune System

Biological Process

signal transduction
cell surface receptor signaling pathway
positive regulation of cell-cell adhesion
neutrophil degranulation
innate immune response

Molecular Function

protein binding

Cellular Component

plasma membrane
integral component of plasma membrane
cell surface
secretory granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381605
Coding exons: 5
Length: 56541
Individuals with no LoFs: 125582
Homozygous LoFs: 0
Heterozygous LoFs: 166
Defined: 125748
p: 0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.582	255	230	1.11	0.0000137	2547
Missense (PolyPhen)		45	48.117	0.93522		625
Synonymous	-2.13	121	94.6	1.28	0.00000580	847
Loss of Function	-0.357	17	15.5	1.10	7.51e-7	172

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0031	0.0030	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.0018	0.0018	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.0943

Intolerance Scores

LoFtool: 0.970
RVIS EVS: 3.22
RVIS percentile EVS: 99.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.458

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium