STAP1
Basic information
Region (hg38): 4:67558726-67607337
Links
Phenotypes
GenCC
Source:
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 STAP1 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 | 26 | 28 | ||||
missense | 57 | 61 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 12 | 19 | ||||
Total | 0 | 1 | 57 | 35 | 15 |
Variants in STAP1
This is a list of pathogenic ClinVar variants found in the STAP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-67558807-G-T | STAP1-related disorder | Likely benign (Nov 30, 2020) | ||
4-67558814-T-C | STAP1-related disorder | Benign (Feb 20, 2019) | ||
4-67558823-A-G | not specified | Uncertain significance (May 22, 2023) | ||
4-67558828-C-A | not specified | Uncertain significance (May 08, 2023) | ||
4-67558843-C-G | not specified | Uncertain significance (Aug 07, 2021) | ||
4-67558851-C-A | not specified | Likely benign (Aug 24, 2019) | ||
4-67558859-A-G | not specified | Uncertain significance (Feb 02, 2022) | ||
4-67558866-A-G | not specified | Likely benign (Nov 08, 2023) | ||
4-67558877-C-T | Uncertain significance (-) | |||
4-67558895-A-C | not specified | Uncertain significance (Feb 06, 2024) | ||
4-67558915-C-T | not specified | Uncertain significance (Mar 21, 2022) | ||
4-67558916-G-A | not specified | Uncertain significance (Jun 09, 2024) | ||
4-67558922-G-C | not specified | Uncertain significance (Oct 09, 2022) | ||
4-67558927-C-T | not specified | Uncertain significance (Dec 04, 2022) | ||
4-67558928-G-A | not specified | Likely benign (Jul 12, 2021) | ||
4-67558935-T-C | STAP1-related disorder | Benign/Likely benign (Aug 07, 2020) | ||
4-67570858-T-C | Benign (Sep 21, 2018) | |||
4-67570978-C-T | Likely benign (Sep 29, 2018) | |||
4-67571090-G-A | not specified | Likely benign (Aug 10, 2021) | ||
4-67571102-A-G | Hypercholesterolemia, familial, 1 | Likely pathogenic (-) | ||
4-67571107-G-A | not specified | Likely benign (Jul 19, 2020) | ||
4-67571108-T-C | not specified | Likely benign (Nov 17, 2022) | ||
4-67571117-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
4-67571120-A-C | not specified | Uncertain significance (Mar 08, 2024) | ||
4-67571121-C-T | not specified | Uncertain significance (May 30, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
STAP1 | protein_coding | protein_coding | ENST00000265404 | 9 | 48610 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000170 | 0.885 | 125708 | 0 | 39 | 125747 | 0.000155 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0251 | 155 | 156 | 0.994 | 0.00000816 | 1932 |
Missense in Polyphen | 35 | 46.265 | 0.75651 | 546 | ||
Synonymous | -1.16 | 64 | 53.3 | 1.20 | 0.00000278 | 523 |
Loss of Function | 1.50 | 10 | 16.6 | 0.602 | 8.56e-7 | 218 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000522 | 0.000521 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000219 | 0.000217 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000196 | 0.000193 |
Middle Eastern | 0.000219 | 0.000217 |
South Asian | 0.00 | 0.00 |
Other | 0.000344 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: In BCR signaling, appears to function as a docking protein acting downstream of TEC and participates in a positive feedback loop by increasing the activity of TEC. {ECO:0000269|PubMed:10518561}.;
- Pathway
- BCR;Signaling events mediated by Stem cell factor receptor (c-Kit)
(Consensus)
Recessive Scores
- pRec
- 0.0976
Intolerance Scores
- loftool
- 0.563
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.44
Haploinsufficiency Scores
- pHI
- 0.663
- hipred
- N
- hipred_score
- 0.245
- ghis
- 0.634
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.760
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stap1
- Phenotype
Gene ontology
- Biological process
- transmembrane receptor protein tyrosine kinase signaling pathway;positive regulation of gene expression;negative regulation of macrophage chemotaxis;negative regulation of phosphorylation;positive regulation of B cell receptor signaling pathway;positive regulation of phagocytosis, engulfment;cellular response to lipopolysaccharide;negative regulation of ruffle assembly;negative regulation of macrophage colony-stimulating factor signaling pathway;positive regulation of microglial cell activation;positive regulation of non-membrane spanning protein tyrosine kinase activity;negative regulation of microglial cell migration;positive regulation of microglial cell mediated cytotoxicity;positive regulation of actin cytoskeleton reorganization
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrion;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- phosphotyrosine residue binding;transmembrane receptor protein tyrosine kinase adaptor activity;SH3/SH2 adaptor activity;macrophage colony-stimulating factor receptor binding;protein binding;phospholipid binding;protein kinase binding