PRIMPOL
Basic information
Region (hg38): 4:184649667-184694963
Previous symbols: [ "CCDC111" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Myopia 22, autosomal dominant | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Ophthalmologic | 23579484 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRIMPOL 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 | 1 | |||||
missense | 48 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 0 | 0 | 50 | 4 | 1 |
Variants in PRIMPOL
This is a list of pathogenic ClinVar variants found in the PRIMPOL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-184657144-A-G | PRIMPOL-related disorder | Uncertain significance (May 12, 2023) | ||
4-184657173-A-T | PRIMPOL-related disorder | Benign (Feb 12, 2024) | ||
4-184657200-G-T | not specified | Uncertain significance (Jan 09, 2024) | ||
4-184657219-G-A | not specified | Uncertain significance (Nov 07, 2024) | ||
4-184657253-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
4-184657256-C-T | not specified | Uncertain significance (May 29, 2024) | ||
4-184657288-C-G | not specified | Uncertain significance (Apr 10, 2023) | ||
4-184659349-G-A | PRIMPOL-related disorder | Uncertain significance (Aug 07, 2024) | ||
4-184659367-A-G | not specified | Uncertain significance (Mar 19, 2024) | ||
4-184659378-T-C | PRIMPOL-related disorder | Likely benign (Apr 09, 2018) | ||
4-184659380-G-A | not specified | Uncertain significance (Aug 11, 2024) | ||
4-184659386-G-A | not specified | Uncertain significance (Oct 20, 2023) | ||
4-184659403-A-G | Benign (Aug 04, 2018) | |||
4-184659422-T-G | not specified | Uncertain significance (Oct 16, 2024) | ||
4-184659424-T-G | Myopia 22, autosomal dominant • not specified | Uncertain significance (May 04, 2022) | ||
4-184659428-A-G | not specified | Uncertain significance (Dec 22, 2023) | ||
4-184659440-A-G | PRIMPOL-related disorder | Likely benign (Aug 08, 2019) | ||
4-184661787-C-T | not specified | Uncertain significance (Aug 18, 2021) | ||
4-184661800-T-C | PRIMPOL-related disorder | Benign (May 06, 2024) | ||
4-184661848-A-G | not specified | Uncertain significance (Oct 10, 2023) | ||
4-184661860-A-T | not specified | Uncertain significance (Oct 22, 2024) | ||
4-184661873-T-G | not specified | Uncertain significance (Mar 25, 2024) | ||
4-184666010-C-T | not specified | Uncertain significance (Sep 26, 2022) | ||
4-184666032-A-G | not specified | Likely benign (Jul 21, 2021) | ||
4-184672198-G-T | not specified | Uncertain significance (Jul 04, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PRIMPOL | protein_coding | protein_coding | ENST00000314970 | 12 | 45351 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.33e-18 | 0.00542 | 125130 | 2 | 614 | 125746 | 0.00245 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.299 | 297 | 283 | 1.05 | 0.0000137 | 3705 |
Missense in Polyphen | 97 | 93.992 | 1.032 | 1252 | ||
Synonymous | 0.244 | 96 | 99.1 | 0.969 | 0.00000478 | 990 |
Loss of Function | 0.157 | 28 | 28.9 | 0.969 | 0.00000148 | 377 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00192 | 0.00191 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0134 | 0.0134 |
Finnish | 0.00134 | 0.00134 |
European (Non-Finnish) | 0.000773 | 0.000765 |
Middle Eastern | 0.0134 | 0.0134 |
South Asian | 0.00666 | 0.00662 |
Other | 0.00115 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: DNA primase and DNA polymerase able to initiate de novo DNA synthesis using dNTPs. Shows a high capacity to tolerate DNA damage lesions such as 8oxoG and abasic sites in DNA. Involved in translesion synthesis via its primase activity by mediating uninterrupted fork progression after programmed or damage-induced fork arrest and by reinitiating DNA synthesis after dNTP depletion. Required for mitochondrial DNA (mtDNA) synthesis, suggesting it may be involved in DNA tolerance during the replication of mitochondrial DNA. Has non-overlapping function with POLH. {ECO:0000269|PubMed:24126761, ECO:0000269|PubMed:24207056, ECO:0000269|PubMed:24240614, ECO:0000269|PubMed:24267451}.;
- Disease
- DISEASE: Myopia 22, autosomal dominant (MYP22) [MIM:615420]: A refractive error of the eye, in which parallel rays from a distant object come to focus in front of the retina, vision being better for near objects than for far. {ECO:0000269|PubMed:23579484}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- loftool
- rvis_EVS
- 0.51
- rvis_percentile_EVS
- 80.24
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- N
- hipred_score
- 0.219
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Primpol
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; reproductive system phenotype; pigmentation phenotype; vision/eye phenotype; immune system phenotype; cellular phenotype;
Gene ontology
- Biological process
- mitochondrial DNA replication;DNA replication, synthesis of RNA primer;response to UV;translesion synthesis;replication fork processing
- Cellular component
- nucleus;mitochondrial matrix
- Molecular function
- chromatin binding;DNA-directed DNA polymerase activity;DNA primase activity;protein binding;manganese ion binding