ERAP2

endoplasmic reticulum aminopeptidase 2, the group of Aminopeptidases|M1 metallopeptidases

Basic information

Region (hg38): 5:96875985-96919703

Links

ENSG00000164308 ∙ NCBI:64167 ∙ OMIM:609497 ∙ HGNC:29499 ∙ Uniprot:Q6P179 ∙ 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 ERAP2 gene.

• Inborn genetic diseases (36 variants)
• not provided (10 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERAP2 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				2	2	4
missense			35	3	2	40
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	36	5	5

Variants in ERAP2

This is a list of pathogenic ClinVar variants found in the ERAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-96879701-G-A		not specified	Uncertain significance (Jan 08, 2024)
5-96879768-T-C		not specified	Uncertain significance (Sep 17, 2021)
5-96879774-C-A		not specified	Uncertain significance (Nov 17, 2022)
5-96879799-C-G		not specified	Uncertain significance (Jan 05, 2022)
5-96879813-G-C		not specified	Uncertain significance (Jan 27, 2022)
5-96879861-G-T		not specified	Uncertain significance (Feb 17, 2024)
5-96879870-T-A			Likely benign (Dec 18, 2017)
5-96879977-G-A		not specified	Uncertain significance (Aug 30, 2022)
5-96880014-T-C		not specified	Uncertain significance (Aug 22, 2023)
5-96883830-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-96883853-G-T			Uncertain significance (Apr 01, 2023)
5-96883861-G-C		not specified	Uncertain significance (Sep 20, 2023)
5-96886656-T-C			Benign (Feb 20, 2018)
5-96886709-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-96886775-T-G		not specified	Uncertain significance (Mar 16, 2022)
5-96889193-C-G		not specified	Uncertain significance (Jun 24, 2022)
5-96889212-C-T		not specified	Likely benign (Jun 29, 2022)
5-96889219-A-T		not specified	Uncertain significance (Oct 21, 2021)
5-96889244-A-G			Likely benign (Apr 01, 2023)
5-96895297-G-A		not specified	Uncertain significance (Nov 10, 2022)
5-96895352-T-G		not specified	Benign/Likely benign (Aug 01, 2023)
5-96896395-G-A			Benign (Aug 01, 2018)
5-96896421-T-C			Benign (May 21, 2018)
5-96896452-C-T		not specified	Uncertain significance (Jun 03, 2022)
5-96896789-G-C		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERAP2	protein_coding	protein_coding	ENST00000437043	18	43778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-28	0.000408	125299	2	447	125748	0.00179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0715	501	497	1.01	0.0000243	6323
Missense in Polyphen		189	169.17	1.1172		2287
Synonymous	0.150	183	186	0.986	0.00000970	1782
Loss of Function	0.461	45	48.5	0.929	0.00000233	608

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00350	0.00349
Ashkenazi Jewish	0.00350	0.00348
East Asian	0.00227	0.00223
Finnish	0.000324	0.000323
European (Non-Finnish)	0.00188	0.00185
Middle Eastern	0.00227	0.00223
South Asian	0.00251	0.00242
Other	0.00135	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I- binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys. {ECO:0000269|PubMed:12799365, ECO:0000269|PubMed:15908954, ECO:0000269|PubMed:16286653}.

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.995
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.7

Haploinsufficiency Scores

• pHI: 0.385
• hipred: N
• hipred_score: 0.144
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response;antigen processing and presentation of peptide antigen via MHC class I;proteolysis;regulation of blood pressure;antigen processing and presentation of endogenous peptide antigen via MHC class I;peptide catabolic process
• Cellular component: cytoplasm;endoplasmic reticulum lumen;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: endopeptidase activity;aminopeptidase activity;metallopeptidase activity;zinc ion binding;peptide binding;metalloaminopeptidase activity