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GeneBe

RNPEPL1

arginyl aminopeptidase like 1, the group of M1 metallopeptidases

Basic information

Region (hg38): 2:240565803-240581372

Links

ENSG00000142327NCBI:57140OMIM:605287HGNC:10079Uniprot:Q9HAU8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNPEPL1 gene.

  • Inborn genetic diseases (34 variants)
  • not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNPEPL1 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
2
clinvar
3
missense
33
clinvar
1
clinvar
1
clinvar
35
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
0
Total 0 0 33 2 3

Variants in RNPEPL1

This is a list of pathogenic ClinVar variants found in the RNPEPL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-240568651-C-T Inborn genetic diseases Uncertain significance (Sep 16, 2021)2364617
2-240568692-G-T Inborn genetic diseases Uncertain significance (Jun 18, 2021)2344621
2-240568795-C-A Inborn genetic diseases Uncertain significance (Jul 20, 2021)2343854
2-240568855-T-G Inborn genetic diseases Uncertain significance (Dec 13, 2021)2266339
2-240568872-G-A Inborn genetic diseases Uncertain significance (May 24, 2023)2515100
2-240568906-C-G Inborn genetic diseases Uncertain significance (May 03, 2023)2543125
2-240568906-C-T Inborn genetic diseases Uncertain significance (Jan 07, 2022)2390520
2-240568908-G-T Inborn genetic diseases Uncertain significance (May 27, 2022)2388205
2-240568918-C-A Inborn genetic diseases Uncertain significance (Jun 24, 2022)2378053
2-240568921-G-A Inborn genetic diseases Uncertain significance (Jan 10, 2022)2396986
2-240568923-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2022)2216960
2-240568953-C-T Inborn genetic diseases Uncertain significance (Oct 12, 2022)2222107
2-240568971-G-A Inborn genetic diseases Uncertain significance (Aug 21, 2023)2619884
2-240568992-G-T Inborn genetic diseases Uncertain significance (Jul 30, 2023)2614886
2-240569070-C-T Inborn genetic diseases Uncertain significance (Jun 07, 2023)2558390
2-240569071-C-T Inborn genetic diseases Uncertain significance (Aug 08, 2023)2597160
2-240569100-A-G Inborn genetic diseases Uncertain significance (Oct 26, 2022)2320106
2-240572483-G-A Inborn genetic diseases Uncertain significance (Dec 03, 2021)2264391
2-240573117-C-T Inborn genetic diseases Uncertain significance (Oct 06, 2021)2371162
2-240573146-C-T Inborn genetic diseases Uncertain significance (Apr 25, 2022)2212574
2-240573147-G-A Inborn genetic diseases Likely benign (Nov 22, 2021)2214619
2-240573164-G-A Benign (Jan 01, 2023)2652091
2-240573229-C-T Benign (Jan 19, 2018)709658
2-240573864-G-A Inborn genetic diseases Uncertain significance (Sep 15, 2021)2386788
2-240574187-C-T Inborn genetic diseases Uncertain significance (Dec 13, 2021)2266502

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNPEPL1protein_codingprotein_codingENST00000270357 915569
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00004120.9911257120161257280.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.222023130.6460.00002113182
Missense in Polyphen64114.140.560711078
Synonymous-0.6251521431.070.00001051011
Loss of Function2.331123.10.4770.00000108240

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001260.000123
Ashkenazi Jewish0.00009940.0000992
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00007990.0000791
Middle Eastern0.0001090.000109
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Broad specificity aminopeptidase which preferentially hydrolyzes an N-terminal methionine, citrulline or glutamine. {ECO:0000269|PubMed:19508204}.;

Recessive Scores

pRec
0.111

Haploinsufficiency Scores

pHI
0.207
hipred
Y
hipred_score
0.639
ghis
0.584

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.415

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnpepl1
Phenotype

Gene ontology

Biological process
proteolysis
Cellular component
Molecular function
zinc ion binding;metalloaminopeptidase activity