OSTF1
Basic information
Region (hg38): 9:75088514-75147265
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSTF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012383.5. 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 | 0 | |||||
missense | 22 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 22 | 0 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OSTF1 | protein_coding | protein_coding | ENST00000346234 | 10 | 58723 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00166 | 0.974 | 125730 | 0 | 15 | 125745 | 0.0000596 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.431 | 99 | 112 | 0.885 | 0.00000535 | 1399 |
Missense in Polyphen | 22 | 40.51 | 0.54308 | 542 | ||
Synonymous | 0.983 | 34 | 42.1 | 0.807 | 0.00000223 | 377 |
Loss of Function | 1.98 | 7 | 15.4 | 0.456 | 7.16e-7 | 188 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000721 | 0.0000721 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000555 | 0.0000544 |
Finnish | 0.000140 | 0.0000924 |
European (Non-Finnish) | 0.0000899 | 0.0000791 |
Middle Eastern | 0.0000555 | 0.0000544 |
South Asian | 0.0000705 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Induces bone resorption, acting probably through a signaling cascade which results in the secretion of factor(s) enhancing osteoclast formation and activity. {ECO:0000269|PubMed:10092216}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.215
Intolerance Scores
- loftool
- 0.426
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.156
- hipred
- Y
- hipred_score
- 0.595
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.883
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ostf1
- Phenotype
- skeleton phenotype;
Gene ontology
- Biological process
- ossification;signal transduction;neutrophil degranulation
- Cellular component
- extracellular region;secretory granule lumen;ficolin-1-rich granule lumen
- Molecular function
- protein binding;SH3 domain binding