ORC5

origin recognition complex subunit 5, the group of Origin recognition complex |Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 7:104126341-104208047

Previous symbols: [ "ORC5L" ]

Links

ENSG00000164815 ∙ NCBI:5001 ∙ OMIM:602331 ∙ HGNC:8491 ∙ Uniprot:O43913 ∙ 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 ORC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORC5 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in ORC5

This is a list of pathogenic ClinVar variants found in the ORC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-104136845-C-G		not specified	Uncertain significance (Dec 20, 2023)
7-104136877-G-A		not specified	Uncertain significance (Aug 11, 2022)
7-104161085-T-C		not specified	Uncertain significance (Jul 15, 2021)
7-104161121-T-C		not specified	Uncertain significance (Dec 03, 2021)
7-104161128-T-C		not specified	Uncertain significance (Sep 23, 2023)
7-104165245-T-A		not specified	Uncertain significance (Mar 28, 2022)
7-104166851-T-C		not specified	Uncertain significance (Oct 16, 2023)
7-104166864-C-A		not specified	Uncertain significance (Apr 13, 2022)
7-104166867-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-104168487-G-A		not specified	Uncertain significance (May 28, 2023)
7-104168501-T-G		not specified	Uncertain significance (Mar 11, 2022)
7-104183961-T-C		not specified	Uncertain significance (Jul 20, 2021)
7-104188324-T-C		not specified	Uncertain significance (Jul 20, 2021)
7-104195154-T-C		not specified	Uncertain significance (Dec 21, 2023)
7-104195199-C-T		not specified	Uncertain significance (Aug 04, 2023)
7-104197766-C-G		not specified	Uncertain significance (Jun 18, 2024)
7-104197767-C-A		not specified	Uncertain significance (Jun 18, 2024)
7-104200861-T-A		not specified	Uncertain significance (Jul 17, 2023)
7-104200862-C-A		not specified	Uncertain significance (Jul 17, 2023)
7-104200901-G-C		not specified	Uncertain significance (Nov 30, 2022)
7-104200917-C-G		not specified	Uncertain significance (Mar 15, 2024)
7-104204233-C-T		not specified	Uncertain significance (Mar 18, 2024)
7-104207862-C-G		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ORC5	protein_coding	protein_coding	ENST00000297431	14	81708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000212	0.976	125694	0	46	125740	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	194	220	0.881	0.0000108	2843
Missense in Polyphen		48	59.725	0.80369		782
Synonymous	-2.28	108	81.8	1.32	0.00000430	793
Loss of Function	2.08	13	24.0	0.542	0.00000108	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000551	0.000551
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.0000483	0.0000462
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000329	0.000326
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent. The specific DNA sequences that define origins of replication have not been identified yet. ORC is required to assemble the pre- replication complex necessary to initiate DNA replication.
• Pathway: Cell cycle - Homo sapiens (human);Cell Cycle;G1 to S cell cycle control;DNA Replication;cdk regulation of dna replication;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;Synthesis of DNA;S Phase;G1/S Transition;E2F-enabled inhibition of pre-replication complex formation;Assembly of the ORC complex at the origin of replication;CDC6 association with the ORC:origin complex;CDT1 association with the CDC6:ORC:origin complex;Assembly of the pre-replicative complex;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.980
• hipred: Y
• hipred_score: 0.725
• ghis: 0.671

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Orc5

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;DNA replication;DNA replication initiation
• Cellular component: nuclear chromosome, telomeric region;origin recognition complex;nucleus;nucleoplasm;nuclear origin of replication recognition complex;cytosol
• Molecular function: nucleotide binding;molecular_function;DNA replication origin binding;protein binding;ATP binding