OSTF1

protein-coding

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

Gene summary

Osteoclast-stimulating factor-1 is an intracellular protein produced by osteoclasts that indirectly induces osteoclast formation and bone resorption (Reddy et al., 1998 [PubMed 10092216]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_012383.5

Inheritance

—

ClinVar variants

U:33

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr9:75,088,514-75,147,265

External References & Databases

Ensembl (ENSG00000134996)

Transcript & Mutation Effects

hg38 • Region Span ~58.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OSTF1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012383.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			28 clinvar			28
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	33	0	0	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012383.5	RefSeq	NP_036515.4	10	MANE Select
ENST00000346234.7	Ensembl	ENSP00000340836.6	10	MANE Select
ENST00000857341.1	Ensembl	ENSP00000527400.1	9	Standard
ENST00000857341.2	Ensembl	ENSP00000527400.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

ossification
signal transduction
neutrophil degranulation

Molecular Function

protein binding
SH3 domain binding

Cellular Component

extracellular region
secretory granule lumen
ficolin-1-rich granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000346234
Coding exons: 10
Length: 58723
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125745
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.431	99	112	0.885	0.00000535	1399
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000072	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000054	rare
Finnish	0.00014	0.000092	rare
European (Non-Finnish)	0.000090	0.000079	rare
South Asian	0.000071	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.215

Intolerance Scores

LoFtool: 0.426
RVIS EVS: -0.27
RVIS percentile EVS: 33.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.883

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium