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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.

  • Inborn genetic diseases (36 variants)
  • not provided (2 variants)

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
36
clinvar
1
clinvar
37
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 36 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 Inborn genetic diseases Uncertain significance (Oct 06, 2021)2253386
1-201982737-A-T Inborn genetic diseases Uncertain significance (Jul 05, 2023)2609465
1-201982811-C-T Inborn genetic diseases Uncertain significance (Feb 16, 2023)2486248
1-201982847-G-T Inborn genetic diseases Uncertain significance (Jan 31, 2022)2274753
1-201982853-G-A Inborn genetic diseases Uncertain significance (Sep 30, 2021)2390057
1-201982956-G-T Inborn genetic diseases Uncertain significance (Jun 18, 2021)2343204
1-201983040-C-T Inborn genetic diseases Uncertain significance (Jul 13, 2021)2358371
1-201983063-G-T Inborn genetic diseases Uncertain significance (May 18, 2022)2211068
1-201988922-G-A Inborn genetic diseases Uncertain significance (Sep 17, 2021)2251596
1-201989008-G-A Benign (Jul 23, 2018)767743
1-201989015-G-A Inborn genetic diseases Uncertain significance (Apr 19, 2023)2509712
1-201989040-T-C Inborn genetic diseases Uncertain significance (Mar 29, 2023)2531644
1-201996202-G-A Inborn genetic diseases Uncertain significance (Jun 29, 2023)2608933
1-201996208-A-G Inborn genetic diseases Uncertain significance (May 31, 2023)2509147
1-201996238-C-T Inborn genetic diseases Uncertain significance (May 25, 2022)2291009
1-201996239-T-C Inborn genetic diseases Uncertain significance (Nov 08, 2021)2347871
1-201997360-G-A Inborn genetic diseases Uncertain significance (Oct 22, 2021)2256521
1-201997393-C-T Inborn genetic diseases Uncertain significance (Aug 28, 2023)2622160
1-201997413-C-T Benign (Jul 23, 2018)712095
1-201997416-T-A Inborn genetic diseases Uncertain significance (Apr 25, 2022)2215979
1-201997493-A-C Inborn genetic diseases Uncertain significance (Jul 21, 2021)2239123
1-201997504-A-G Inborn genetic diseases Uncertain significance (Mar 03, 2022)2206480
1-201997524-G-A Inborn genetic diseases Uncertain significance (Apr 04, 2023)2513173
1-201999904-G-A Inborn genetic diseases Uncertain significance (Nov 18, 2022)2327477
1-201999913-A-T Inborn genetic diseases Uncertain significance (Apr 25, 2022)2285594

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