OSTF1

osteoclast stimulating factor 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 9:75088514-75147265

Links

ENSG00000134996 ∙ NCBI:26578 ∙ OMIM:610180 ∙ HGNC:8510 ∙ Uniprot:Q92882 ∙ 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 OSTF1 gene.

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.

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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in OSTF1

This is a list of pathogenic ClinVar variants found in the OSTF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-75130581-G-A		not specified	Uncertain significance (Sep 26, 2022)
9-75130600-G-C		not specified	Uncertain significance (Aug 02, 2023)
9-75130632-A-G		not specified	Uncertain significance (Sep 27, 2022)
9-75133300-T-G		not specified	Uncertain significance (Mar 30, 2024)
9-75133399-A-G		not specified	Uncertain significance (Apr 27, 2024)
9-75134351-G-C		not specified	Uncertain significance (Mar 29, 2024)
9-75137590-A-T		not specified	Uncertain significance (Jun 09, 2022)
9-75140834-G-A		not specified	Uncertain significance (Apr 20, 2023)
9-75140852-G-C		not specified	Uncertain significance (Nov 17, 2022)
9-75140891-A-G		not specified	Uncertain significance (Dec 08, 2023)
9-75146721-G-A		not specified	Uncertain significance (May 10, 2024)
9-75146721-G-T		not specified	Uncertain significance (Aug 23, 2021)
9-75146725-A-G		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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