SIRPG
Basic information
Region (hg38): 20:1629152-1657779
Previous symbols: [ "SIRPB2" ]
Links
Phenotypes
GenCC
Source:
- male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIRPG gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 33 | 37 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 33 | 4 | 2 |
Variants in SIRPG
This is a list of pathogenic ClinVar variants found in the SIRPG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-1629905-T-C | Benign (Oct 17, 2019) | |||
20-1630272-T-A | Benign (Jan 01, 2023) | |||
20-1630274-T-C | not specified | Uncertain significance (Oct 08, 2024) | ||
20-1630304-G-A | not specified | Uncertain significance (Jan 06, 2023) | ||
20-1635269-G-C | not specified | Uncertain significance (Apr 04, 2023) | ||
20-1635428-G-A | not specified | Uncertain significance (May 29, 2024) | ||
20-1635431-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
20-1635455-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
20-1635533-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
20-1635567-T-C | not specified | Uncertain significance (Nov 13, 2023) | ||
20-1636190-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
20-1636218-C-T | not specified | Uncertain significance (Jun 05, 2023) | ||
20-1636220-C-T | not specified | Uncertain significance (Nov 10, 2024) | ||
20-1636241-G-T | not specified | Uncertain significance (May 17, 2023) | ||
20-1636274-C-G | not specified | Uncertain significance (Aug 17, 2022) | ||
20-1636274-C-T | not specified | Likely benign (May 23, 2024) | ||
20-1636275-G-A | not specified | Uncertain significance (May 16, 2024) | ||
20-1636286-G-T | not specified | Uncertain significance (Feb 14, 2024) | ||
20-1636313-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
20-1636326-C-A | not specified | Likely benign (Oct 11, 2024) | ||
20-1636328-A-T | not specified | Uncertain significance (Feb 27, 2024) | ||
20-1636334-T-C | not specified | Uncertain significance (Oct 17, 2023) | ||
20-1636352-T-C | not specified | Uncertain significance (Apr 08, 2024) | ||
20-1636389-A-G | not specified | Uncertain significance (Jun 13, 2024) | ||
20-1636407-C-T | not specified | Likely benign (Feb 03, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SIRPG | protein_coding | protein_coding | ENST00000303415 | 5 | 28628 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.48e-15 | 0.00295 | 125407 | 1 | 340 | 125748 | 0.00136 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.272 | 229 | 218 | 1.05 | 0.0000122 | 2478 |
Missense in Polyphen | 45 | 44.053 | 1.0215 | 617 | ||
Synonymous | -0.877 | 100 | 89.5 | 1.12 | 0.00000536 | 809 |
Loss of Function | -0.849 | 20 | 16.3 | 1.23 | 8.55e-7 | 171 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00369 | 0.00363 |
Ashkenazi Jewish | 0.00139 | 0.00139 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000601 | 0.000601 |
European (Non-Finnish) | 0.00180 | 0.00179 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.00179 | 0.00179 |
dbNSFP
Source:
- Function
- FUNCTION: Probable immunoglobulin-like cell surface receptor. On binding with CD47, mediates cell-cell adhesion. Engagement on T- cells by CD47 on antigen-presenting cells results in enhanced antigen-specific T-cell proliferation and costimulates T-cell activation. {ECO:0000269|PubMed:15383453}.;
- Pathway
- Osteoclast differentiation - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis;Signal regulatory protein family interactions;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.0864
Intolerance Scores
- loftool
- 0.925
- rvis_EVS
- 0.8
- rvis_percentile_EVS
- 87.66
Haploinsufficiency Scores
- pHI
- 0.0760
- hipred
- N
- hipred_score
- 0.133
- ghis
- 0.429
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.108
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- cell adhesion;cell-cell signaling;positive regulation of cell population proliferation;negative regulation of cell population proliferation;positive regulation of cell-cell adhesion;intracellular signal transduction;positive regulation of phagocytosis;positive regulation of T cell activation;leukocyte migration
- Cellular component
- plasma membrane;membrane;integral component of membrane
- Molecular function
- protein binding