RNPEPL1

arginyl aminopeptidase like 1, the group of M1 metallopeptidases

Basic information

Region (hg38): 2:240565803-240581372

Links

ENSG00000142327 ∙ NCBI:57140 ∙ OMIM:605287 ∙ HGNC:10079 ∙ Uniprot:Q9HAU8 ∙ 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 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	2	3
missense			33	1	1	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		not specified	Uncertain significance (Sep 16, 2021)
2-240568692-G-T		not specified	Uncertain significance (Jun 18, 2021)
2-240568759-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-240568795-C-A		not specified	Uncertain significance (Jul 20, 2021)
2-240568806-G-C		not specified	Uncertain significance (Dec 30, 2023)
2-240568855-T-G		not specified	Uncertain significance (Dec 13, 2021)
2-240568872-G-A		not specified	Uncertain significance (May 24, 2023)
2-240568906-C-G		not specified	Uncertain significance (May 03, 2023)
2-240568906-C-T		not specified	Uncertain significance (Jan 07, 2022)
2-240568908-G-T		not specified	Uncertain significance (May 27, 2022)
2-240568918-C-A		not specified	Uncertain significance (Jun 24, 2022)
2-240568920-G-C		not specified	Uncertain significance (Dec 27, 2023)
2-240568921-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-240568923-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-240568935-C-T		not specified	Uncertain significance (Nov 12, 2021)
2-240568953-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-240568971-G-A		not specified	Uncertain significance (Aug 21, 2023)
2-240568992-G-T		not specified	Uncertain significance (Jul 30, 2023)
2-240569070-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-240569071-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-240569100-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-240572483-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-240573117-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-240573146-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-240573147-G-A		not specified	Likely benign (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNPEPL1	protein_coding	protein_coding	ENST00000270357	9	15569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000412	0.991	125712	0	16	125728	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	202	313	0.646	0.0000211	3182
Missense in Polyphen		64	114.14	0.56071		1078
Synonymous	-0.625	152	143	1.07	0.0000105	1011
Loss of Function	2.33	11	23.1	0.477	0.00000108	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000123
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rnpepl1

Gene ontology

• Biological process: proteolysis
• Molecular function: zinc ion binding;metalloaminopeptidase activity