SIRPB1
Basic information
Region (hg38): 20:1561385-1620061
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | |||||
missense | 52 | 59 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 52 | 10 | 0 |
GnomAD
Source:
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:
- 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
- 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