RNPEP

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

Basic information

Region (hg38): 1:201982372-202006147

Links

ENSG00000176393 ∙ NCBI:6051 ∙ OMIM:602675 ∙ HGNC:10078 ∙ Uniprot:Q9H4A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	1
missense			54		1	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: gnomAD

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: 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

• 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

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