ORC3
protein-codingorigin recognition complex subunit 3, the group of Origin recognition complex
Gene summary
The origin recognition complex (ORC) is a highly conserved six subunits protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins. The protein encoded by this gene is a subunit of the ORC complex. Studies of a similar gene in Drosophila suggested a possible role of this protein in neuronal proliferation and olfactory memory. Alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene. [provided by RefSeq, Jul 2008]
- ORC3L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~87.8 kbGenCC 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 ORC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012381.4. 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 | 1 | 3 | |||
| missense | 1 | 105 | 5 | 111 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 1 | 111 | 6 | 0 | 118 |
Highest pathogenic variant AF is 0.00003538733
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036513.2 | 20 | MANE Select | |
| Ensembl | ENSP00000376586.3 | 20 | MANE Select | |
| RefSeq | NP_001184188.1 | 15 | Standard | |
| RefSeq | NP_862820.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell cycle - Homo sapiens (human)
- Cell Cycle
- G1 to S cell cycle control
- DNA Replication
- cdk regulation of dna replication
Biological Process
- G1/S transition of mitotic cell cycle
- DNA replication
- pre-replicative complex assembly involved in nuclear cell cycle DNA replication
- DNA replication initiation
- neural precursor cell proliferation
Molecular Function
- DNA replication origin binding
- protein binding
Cellular Component
- nuclear chromosome, telomeric region
- origin recognition complex
- nucleoplasm
- nuclear pre-replicative complex
- nuclear origin of replication recognition complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000257789
- Coding exons
- 20
- Length
- 77331
- Individuals with no LoFs
- 125663
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 84
- Defined
- 125747
- p
- 0.000334
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.515 | 330 | 357 | 0.923 | 0.0000173 | 4685 |
| Missense (PolyPhen) | 87 | 105.54 | 0.82437 | 1453 | ||
| Synonymous | 0.298 | 128 | 132 | 0.967 | 0.00000699 | 1288 |
| Loss of Function | 3.12 | 22 | 44.4 | 0.495 | 0.00000233 | 553 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00099 | 0.00099 | rare |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00041 | 0.00040 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.0010 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
- 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. Binds histone H3 and H4 trimethylation marks H3K9me3, H3K27me3 and H4K20me3. {ECO:0000269|PubMed:22427655}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- RVIS EVS
- 0.67
- RVIS percentile EVS
- 84.64
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |