RNPEP

arginyl aminopeptidase, the group of MicroRNA protein coding host genes|Aminopeptidases|M1 metallopeptidases

Basic information

Region (hg38): 1:201982371-202006147

Links

ENSG00000176393NCBI:6051OMIM:602675HGNC:10078Uniprot:Q9H4A4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNPEP gene.

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
clinvar
1
missense
54
clinvar
1
clinvar
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)2253386
1-201982707-G-A not specified Uncertain significance (Dec 18, 2023)3155540
1-201982737-A-T not specified Uncertain significance (Jul 05, 2023)2609465
1-201982769-G-A not specified Uncertain significance (Feb 27, 2024)3155529
1-201982811-C-T not specified Uncertain significance (Feb 16, 2023)2486248
1-201982818-G-A not specified Uncertain significance (Jan 17, 2024)3155533
1-201982847-G-T not specified Uncertain significance (Jan 31, 2022)2274753
1-201982853-G-A not specified Uncertain significance (Sep 30, 2021)2390057
1-201982944-T-C not specified Uncertain significance (Feb 05, 2024)3155539
1-201982956-G-T not specified Uncertain significance (Jun 18, 2021)2343204
1-201983040-C-T not specified Uncertain significance (Jul 13, 2021)2358371
1-201983063-G-T not specified Uncertain significance (May 18, 2022)2211068
1-201983100-G-A not specified Uncertain significance (Aug 26, 2022)3155541
1-201988922-G-A not specified Uncertain significance (Sep 17, 2021)2251596
1-201988982-C-T not specified Uncertain significance (Jan 24, 2024)3155543
1-201989008-G-A Benign (Jul 23, 2018)767743
1-201989015-G-A not specified Uncertain significance (Apr 19, 2023)2509712
1-201989040-T-C not specified Uncertain significance (Mar 29, 2023)2531644
1-201989448-C-G not specified Uncertain significance (Apr 23, 2024)3314963
1-201996182-C-T not specified Uncertain significance (Jan 17, 2024)3155544
1-201996202-G-A not specified Uncertain significance (Jun 29, 2023)2608933
1-201996208-A-G not specified Uncertain significance (May 31, 2023)2509147
1-201996238-C-T not specified Uncertain significance (May 25, 2022)2291009
1-201996239-T-C not specified Uncertain significance (Mar 04, 2024)2347871
1-201997360-G-A not specified Uncertain significance (Oct 22, 2021)2256521

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNPEPprotein_codingprotein_codingENST00000295640 1123776
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.61e-170.016212549502531257480.00101
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6872863210.8920.00001774192
Missense in Polyphen107131.310.814871636
Synonymous1.021181330.8880.000008061294
Loss of Function0.4322729.50.9140.00000149344

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008030.000742
Ashkenazi Jewish0.006540.00647
East Asian0.0006520.000653
Finnish0.001900.00190
European (Non-Finnish)0.0008900.000888
Middle Eastern0.0006520.000653
South Asian0.0001970.000163
Other0.001480.00147

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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