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

ENSG00000101307 ∙ NCBI:10326 ∙ OMIM:603889 ∙ HGNC:15928 ∙ Uniprot:O00241, Q5TFQ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			52	7		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	10	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIRPB1	protein_coding	protein_coding	ENST00000381605	5	56541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-12	0.0189	125582	0	166	125748	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.582	255	230	1.11	0.0000137	2547
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00114
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00306	0.00305
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00306	0.00305
South Asian	0.00180	0.00180
Other	0.000326	0.000326

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

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

Mouse Genome Informatics

• Gene name: Sirpb1c

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