OIP5

Opa interacting protein 5

Basic information

Region (hg38): 15:41309273-41332591

Links

ENSG00000104147 ∙ NCBI:11339 ∙ OMIM:606020 ∙ HGNC:20300 ∙ Uniprot:O43482 ∙ 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 OIP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OIP5 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in OIP5

This is a list of pathogenic ClinVar variants found in the OIP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41309786-C-A		not specified	Uncertain significance (May 10, 2023)
15-41309816-A-C		not specified	Uncertain significance (Jul 28, 2021)
15-41309831-G-C		not specified	Uncertain significance (Jan 19, 2024)
15-41309848-A-G		not specified	Uncertain significance (Apr 26, 2023)
15-41313284-T-C		not specified	Uncertain significance (Apr 25, 2024)
15-41319684-G-C		not specified	Uncertain significance (Jun 07, 2024)
15-41319700-G-A		not specified	Uncertain significance (Aug 02, 2023)
15-41319709-G-A		not specified	Uncertain significance (Jan 29, 2024)
15-41319715-T-G		not specified	Uncertain significance (Jun 30, 2023)
15-41319734-A-C		not specified	Uncertain significance (May 13, 2024)
15-41331951-G-C		not specified	Uncertain significance (Aug 10, 2021)
15-41332258-C-A		not specified	Uncertain significance (Apr 09, 2024)
15-41332407-G-A		not specified	Uncertain significance (Dec 22, 2023)
15-41332425-C-T		not specified	Uncertain significance (Nov 27, 2023)
15-41332447-A-G		not specified	Uncertain significance (Apr 20, 2023)
15-41332492-T-G		not specified	Uncertain significance (May 27, 2022)
15-41332504-A-T		not specified	Uncertain significance (Mar 18, 2024)
15-41332524-G-A		not specified	Uncertain significance (Dec 21, 2022)
15-41332527-C-T		not specified	Likely benign (Sep 16, 2021)
15-41332530-C-T		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OIP5	protein_coding	protein_coding	ENST00000220514	5	23354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-7	0.124	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.31	171	129	1.32	0.00000602	1458
Missense in Polyphen		56	40.31	1.3892		499
Synonymous	-0.706	61	54.4	1.12	0.00000263	480
Loss of Function	-0.258	10	9.16	1.09	3.89e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000679	0.000669
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000165	0.000163
South Asian	0.000132	0.000131
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for recruitment of CENPA to centromeres and normal chromosome segregation during mitosis. {ECO:0000269|PubMed:17199038}.
• Pathway: Nucleosome assembly;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.0905

Intolerance Scores

• loftool: 0.307
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.493
• hipred: N
• hipred_score: 0.173
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oip5

Gene ontology

• Biological process: cell cycle;chromosome segregation;cell communication;CENP-A containing nucleosome assembly;cell division
• Cellular component: chromosome, centromeric region;chromatin;nucleus;nucleoplasm;cytosol;chromocenter;Cajal body;nuclear speck
• Molecular function: protein binding;identical protein binding;metal ion binding