PRIM2
protein-codingDNA primase subunit 2, the group of MicroRNA protein coding host genes
Gene summary
This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014]
- PRIM2A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~332.0 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 PRIM2 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000947.5. 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 | 3 | 3 | ||||
| missense | 8 | 8 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 15 | 0 | 0 | 15 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000938.2 | 13 | MANE Select | |
| Ensembl | ENSP00000484105.1 | 13 | MANE Select | |
| RefSeq | NP_001269416.1 | 4 | Standard | |
| RefSeq | NP_001269417.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pyrimidine metabolism - Homo sapiens (human)
- DNA replication - Homo sapiens (human)
- Purine metabolism - Homo sapiens (human)
- Pyrimidine metabolism
- G1 to S cell cycle control
Biological Process
- G1/S transition of mitotic cell cycle
- DNA replication, synthesis of RNA primer
- telomere maintenance via semi-conservative replication
Molecular Function
- single-stranded DNA binding
- DNA primase activity
- metal ion binding
- 4 iron, 4 sulfur cluster binding
Cellular Component
- nucleoplasm
- alpha DNA polymerase:primase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000607273
- Coding exons
- 10
- Length
- 333773
- Individuals with no LoFs
- 124586
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 124652
- p
- 0.000265
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.755 | 125 | 151 | 0.827 | 0.00000718 | 2121 |
| Missense (PolyPhen) | 28 | 51.787 | 0.54067 | 727 | ||
| Synonymous | 3.00 | 24 | 51.4 | 0.467 | 0.00000225 | 552 |
| Loss of Function | 1.44 | 14 | 21.2 | 0.661 | 0.00000120 | 260 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.00063 | 0.00058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00037 | 0.00033 | rare |
| Finnish | 0.000099 | 0.000093 | rare |
| European (Non-Finnish) | 0.00013 | 0.00011 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00038 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.;
Recessive Scores
- pRec
- 0.0831
Essentials
- Indispensability pred.
- N
- Indispensability score
- 0.000118
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |