APEH

acylaminoacyl-peptide hydrolase

Basic information

Region (hg38): 3:49674014-49683971

Previous symbols: [ "D3F15S2", "DNF15S2", "D3S48E" ]

Links

ENSG00000164062 ∙ NCBI:327 ∙ OMIM:102645 ∙ HGNC:586 ∙ Uniprot:P13798 ∙ 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 APEH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APEH 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
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in APEH

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

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

Position	Type	Phenotype	Significance	ClinVar
3-49674534-C-A		not specified	Uncertain significance (Jan 24, 2024)
3-49674556-G-T		not specified	Uncertain significance (Jun 07, 2023)
3-49675266-G-A		not specified	Uncertain significance (Sep 14, 2023)
3-49675303-G-C		not specified	Uncertain significance (Apr 25, 2023)
3-49675744-A-G		not specified	Uncertain significance (Dec 14, 2023)
3-49675755-A-C		not specified	Uncertain significance (Dec 16, 2023)
3-49675756-C-T		not specified	Uncertain significance (May 06, 2024)
3-49675925-A-G		not specified	Uncertain significance (Apr 25, 2023)
3-49676174-C-T			Likely benign (Apr 01, 2022)
3-49676180-T-A		not specified	Uncertain significance (Aug 08, 2023)
3-49676498-A-C		not specified	Uncertain significance (Oct 03, 2022)
3-49676679-T-A		not specified	Uncertain significance (Feb 07, 2023)
3-49676694-A-G		not specified	Uncertain significance (May 08, 2024)
3-49676812-A-C		not specified	Uncertain significance (Jul 30, 2023)
3-49676941-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-49676963-G-T		not specified	Uncertain significance (May 03, 2023)
3-49678853-G-T		not specified	Uncertain significance (May 17, 2023)
3-49678913-G-C		not specified	Uncertain significance (Jan 17, 2024)
3-49679596-C-G		not specified	Uncertain significance (Feb 10, 2023)
3-49681179-G-A		not specified	Uncertain significance (Nov 10, 2022)
3-49681216-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-49681234-A-C		not specified	Uncertain significance (Oct 05, 2021)
3-49681937-C-G		not specified	Uncertain significance (Jun 12, 2023)
3-49681943-A-C		not specified	Uncertain significance (May 25, 2022)
3-49681961-C-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APEH	protein_coding	protein_coding	ENST00000296456	22	9962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.00e-13	0.984	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	356	426	0.835	0.0000246	4747
Missense in Polyphen		83	120.48	0.68888		1293
Synonymous	1.13	147	166	0.888	0.00000930	1450
Loss of Function	2.48	27	44.9	0.601	0.00000200	508

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000380
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000381	0.000381
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.000381	0.000381
South Asian	0.000361	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This enzyme catalyzes the hydrolysis of the N-terminal peptide bond of an N-acetylated peptide to generate an N- acetylated amino acid and a peptide with a free N-terminus. It preferentially cleaves off Ac-Ala, Ac-Met and Ac-Ser. {ECO:0000269|PubMed:1861871, ECO:0000269|PubMed:2006156}.
• Pathway: Neutrophil degranulation;Eukaryotic Translation Termination;Translation;Metabolism of proteins;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.304

Intolerance Scores

• loftool: 0.724
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.116
• hipred: Y
• hipred_score: 0.554
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apeh

Gene ontology

• Biological process: translational termination;proteolysis;neutrophil degranulation;amyloid-beta metabolic process
• Cellular component: extracellular region;cytosol;nuclear membrane;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: RNA binding;serine-type endopeptidase activity;protein binding;omega peptidase activity;identical protein binding