OIT3

oncoprotein induced transcript 3

Basic information

Region (hg38): 10:72893584-72933036

Links

ENSG00000138315 ∙ NCBI:170392 ∙ OMIM:609330 ∙ HGNC:29953 ∙ Uniprot:Q8WWZ8 ∙ 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 OIT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OIT3 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				2		2
missense			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	5	0

Variants in OIT3

This is a list of pathogenic ClinVar variants found in the OIT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-72893802-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-72893805-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-72893847-G-A		not specified	Uncertain significance (Dec 02, 2022)
10-72893856-G-A		not specified	Likely benign (May 11, 2022)
10-72893857-T-C		not specified	Uncertain significance (Sep 22, 2022)
10-72898687-A-T		not specified	Uncertain significance (Oct 10, 2023)
10-72898761-C-G		not specified	Uncertain significance (Mar 11, 2022)
10-72898800-G-A			Likely benign (Oct 01, 2022)
10-72898851-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-72898864-C-A		not specified	Uncertain significance (Mar 06, 2023)
10-72898906-C-T		not specified	Uncertain significance (May 17, 2023)
10-72898928-A-G		not specified	Uncertain significance (Jun 12, 2023)
10-72898955-C-T		not specified	Uncertain significance (Apr 20, 2024)
10-72899000-T-G		not specified	Uncertain significance (Jul 29, 2022)
10-72899014-G-A		not specified	Uncertain significance (Mar 03, 2022)
10-72900397-G-A		not specified	Uncertain significance (Feb 07, 2023)
10-72900399-G-C		not specified	Uncertain significance (Apr 15, 2024)
10-72900400-G-A		not specified	Uncertain significance (Jul 21, 2021)
10-72900434-G-A		not specified	Uncertain significance (Dec 06, 2022)
10-72900441-C-T			Likely benign (Oct 01, 2022)
10-72900442-G-A		not specified	Uncertain significance (Jun 18, 2021)
10-72906664-C-T		not specified	Uncertain significance (Nov 29, 2023)
10-72906686-G-A		not specified	Uncertain significance (Jun 28, 2022)
10-72911732-A-G		not specified	Uncertain significance (Jan 31, 2023)
10-72911746-G-C		not specified	Uncertain significance (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OIT3	protein_coding	protein_coding	ENST00000334011	9	39453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.39e-11	0.298	125608	0	138	125746	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.965	291	341	0.853	0.0000207	3570
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.00	0.00
East Asian	0.00110	0.00109
Finnish	0.00199	0.00199
European (Non-Finnish)	0.000265	0.000264
Middle Eastern	0.00110	0.00109
South Asian	0.000757	0.000752
Other	0.000327	0.000326

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.314
• hipred: N
• hipred_score: 0.322
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oit3
• Phenotype: renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: urate homeostasis
• Cellular component: nuclear envelope
• Molecular function: calcium ion binding;protein binding