OIT3

protein-coding

oncoprotein induced transcript 3

Gene summary

This gene was identified due to its downregulation in hepatocarcinomas. The encoded protein may be involved in liver development and function. [provided by RefSeq, Sep 2016]

MANE transcript

NM_152635.3

Inheritance

—

ClinVar variants

U:97B:5

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr10:72,893,584-72,933,036

External References & Databases

Ensembl (ENSG00000138315)

Transcript & Mutation Effects

hg38 • Region Span ~39.5 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 OIT3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152635.3. 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			1 clinvar	2 clinvar		3
missense			93 clinvar	3 clinvar		96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	97	5	0	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152635.3	RefSeq	NP_689848.1	9	MANE Select
ENST00000334011.10	Ensembl	ENSP00000333900.5	9	MANE Select
ENST00000622652.1	Ensembl	ENSP00000479787.1	7	Standard
ENST00000622652.2	Ensembl	ENSP00000479787.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

urate homeostasis

Molecular Function

calcium ion binding
protein binding

Cellular Component

nuclear envelope

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334011
Coding exons: 9
Length: 39453
Individuals with no LoFs: 125608
Homozygous LoFs: 0
Heterozygous LoFs: 138
Defined: 125746
p: 0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.965	291	341	0.853	0.0000207	3570
Missense (PolyPhen)		100	130.94	0.7637		1381
Synonymous	0.787	127	139	0.915	0.00000890	1092
Loss of Function	0.965	19	24.1	0.788	0.00000144	260

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0011	0.0011	notable
Finnish	0.0020	0.0020	notable
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00076	0.00075	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in hepatocellular function and development. {ECO:0000269|PubMed:12939600}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.245
RVIS EVS: -1
RVIS percentile EVS: 8.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.246

Gene Damage Prediction

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