RNPEP
Basic information
Region (hg38): 1:201982371-202006147
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 RNPEP 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 | 54 | 55 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 54 | 0 | 2 |
Variants in RNPEP
This is a list of pathogenic ClinVar variants found in the RNPEP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-201982671-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
1-201982707-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
1-201982737-A-T | not specified | Uncertain significance (Jul 05, 2023) | ||
1-201982769-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
1-201982811-C-T | not specified | Uncertain significance (Feb 16, 2023) | ||
1-201982818-G-A | not specified | Uncertain significance (Jan 17, 2024) | ||
1-201982847-G-T | not specified | Uncertain significance (Jan 31, 2022) | ||
1-201982853-G-A | not specified | Uncertain significance (Sep 30, 2021) | ||
1-201982944-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
1-201982956-G-T | not specified | Uncertain significance (Jun 18, 2021) | ||
1-201983040-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
1-201983063-G-T | not specified | Uncertain significance (May 18, 2022) | ||
1-201983100-G-A | not specified | Uncertain significance (Aug 26, 2022) | ||
1-201988922-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
1-201988982-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
1-201989008-G-A | Benign (Jul 23, 2018) | |||
1-201989015-G-A | not specified | Uncertain significance (Apr 19, 2023) | ||
1-201989040-T-C | not specified | Uncertain significance (Mar 29, 2023) | ||
1-201989448-C-G | not specified | Uncertain significance (Apr 23, 2024) | ||
1-201996182-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
1-201996202-G-A | not specified | Uncertain significance (Jun 29, 2023) | ||
1-201996208-A-G | not specified | Uncertain significance (May 31, 2023) | ||
1-201996238-C-T | not specified | Uncertain significance (May 25, 2022) | ||
1-201996239-T-C | not specified | Uncertain significance (Mar 04, 2024) | ||
1-201997360-G-A | not specified | Uncertain significance (Oct 22, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNPEP | protein_coding | protein_coding | ENST00000295640 | 11 | 23776 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.61e-17 | 0.0162 | 125495 | 0 | 253 | 125748 | 0.00101 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.687 | 286 | 321 | 0.892 | 0.0000177 | 4192 |
Missense in Polyphen | 107 | 131.31 | 0.81487 | 1636 | ||
Synonymous | 1.02 | 118 | 133 | 0.888 | 0.00000806 | 1294 |
Loss of Function | 0.432 | 27 | 29.5 | 0.914 | 0.00000149 | 344 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000803 | 0.000742 |
Ashkenazi Jewish | 0.00654 | 0.00647 |
East Asian | 0.000652 | 0.000653 |
Finnish | 0.00190 | 0.00190 |
European (Non-Finnish) | 0.000890 | 0.000888 |
Middle Eastern | 0.000652 | 0.000653 |
South Asian | 0.000197 | 0.000163 |
Other | 0.00148 | 0.00147 |
dbNSFP
Source:
- Function
- FUNCTION: Exopeptidase which selectively removes arginine and/or lysine residues from the N-terminus of several peptide substrates including Arg(0)-Leu-enkephalin, Arg(0)-Met-enkephalin and Arg(- 1)-Lys(0)-somatostatin-14. Can hydrolyze leukotriene A4 (LTA-4) into leukotriene B4 (LTB-4) (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.226
Intolerance Scores
- loftool
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 18.14
Haploinsufficiency Scores
- pHI
- 0.185
- hipred
- N
- hipred_score
- 0.253
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.356
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnpep
- Phenotype
Gene ontology
- Biological process
- proteolysis;negative regulation of blood pressure
- Cellular component
- extracellular region;plasma membrane;secretory granule;extracellular exosome
- Molecular function
- aminopeptidase activity;epoxide hydrolase activity;metalloexopeptidase activity;zinc ion binding