PNRC2
Basic information
Region (hg38): 1:23956838-23963462
Links
Phenotypes
GenCC
Source:
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 PNRC2 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in PNRC2
This is a list of pathogenic ClinVar variants found in the PNRC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-23961467-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 1-23961576-A-G | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-23961597-A-G | not specified | Uncertain significance (Apr 27, 2022) | ||
| 1-23961617-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-23961642-G-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 1-23961672-A-G | not specified | Uncertain significance (Jan 31, 2022) | ||
| 1-23961675-G-A | not specified | Likely benign (Jul 16, 2021) | ||
| 1-23961690-T-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-23961711-T-C | not specified | Uncertain significance (Sep 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PNRC2 | protein_coding | protein_coding | ENST00000334351 | 1 | 4354 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.338 | 0.497 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.186 | 10 | 11.8 | 0.848 | 5.40e-7 | 909 |
| Missense in Polyphen | 4 | 3.5038 | 1.1416 | 204 | ||
| Synonymous | -0.945 | 7 | 4.46 | 1.57 | 2.25e-7 | 248 |
| Loss of Function | 0.666 | 0 | 0.517 | 0.00 | 2.22e-8 | 57 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in nonsense-mediated mRNA decay (NMD) by acting as a bridge between the mRNA decapping complex and the NMD machinery (PubMed:19150429). May act by targeting the NMD machinery to the P-body and recruiting the decapping machinery to aberrant mRNAs (PubMed:19150429). Required for UPF1/RENT1 localization to the P-body (PubMed:19150429). Plays a role in glucocorticoid receptor-mediated mRNA degradation by interacting with the glucocorticoid receptor NR3C1 in a ligand-dependent manner when it is bound to the 5' UTR of target mRNAs and recruiting the RNA helicase UPF1 and the mRNA-decapping enzyme DCP1A, leading to RNA decay (PubMed:25775514). Also acts as a nuclear receptor coactivator (PubMed:11574675). May play a role in controlling the energy balance between energy storage and energy expenditure (By similarity). {ECO:0000250|UniProtKB:Q9CR73, ECO:0000269|PubMed:11574675, ECO:0000269|PubMed:19150429, ECO:0000269|PubMed:25775514}.;
Recessive Scores
- pRec
- 0.112
Haploinsufficiency Scores
- pHI
- 0.621
- hipred
- hipred_score
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Pnrc2
- Phenotype
- liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;deadenylation-independent decapping of nuclear-transcribed mRNA
- Cellular component
- P-body;nucleus;nucleoplasm;Golgi apparatus;cytosol
- Molecular function
- protein binding