PREP

prolyl endopeptidase

Basic information

Region (hg38): 6:105273218-105454062

Links

ENSG00000085377 ∙ NCBI:5550 ∙ OMIM:600400 ∙ HGNC:9358 ∙ Uniprot:P48147 ∙ 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 PREP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PREP 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	1

Variants in PREP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-105278152-T-C		not specified	Uncertain significance (Nov 24, 2024)
6-105278158-C-T		not specified	Uncertain significance (Jul 12, 2023)
6-105278173-G-A		not specified	Uncertain significance (Apr 28, 2022)
6-105278194-C-A		not specified	Uncertain significance (Oct 07, 2024)
6-105278237-G-A			Benign (Jul 13, 2018)
6-105278244-G-A		not specified	Uncertain significance (Apr 15, 2024)
6-105278289-C-T		not specified	Uncertain significance (May 11, 2022)
6-105278293-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-105278338-G-A		not specified	Uncertain significance (Dec 06, 2024)
6-105278398-C-T		not specified	Uncertain significance (Aug 28, 2024)
6-105282519-A-G		not specified	Uncertain significance (Jan 16, 2024)
6-105285525-T-C		not specified	Uncertain significance (May 26, 2022)
6-105288761-T-C		not specified	Uncertain significance (Oct 08, 2024)
6-105288818-G-C		not specified	Uncertain significance (Sep 28, 2022)
6-105288834-T-C		not specified	Uncertain significance (Nov 21, 2024)
6-105288858-T-C		not specified	Uncertain significance (Feb 23, 2023)
6-105323738-T-C		not specified	Uncertain significance (May 26, 2024)
6-105328850-A-C		not specified	Uncertain significance (May 22, 2024)
6-105328904-C-T		not specified	Uncertain significance (Jan 02, 2024)
6-105328915-G-A		not specified	Uncertain significance (May 08, 2024)
6-105328921-G-C		not specified	Uncertain significance (May 30, 2023)
6-105328923-C-G		not specified	Uncertain significance (Oct 12, 2021)
6-105328934-C-T		not specified	Uncertain significance (Dec 15, 2023)
6-105328991-A-T		not specified	Uncertain significance (Jun 24, 2022)
6-105329008-C-T		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PREP	protein_coding	protein_coding	ENST00000369110	15	125520

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0803	0.920	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	277	406	0.683	0.0000220	4695
Missense in Polyphen		47	123.97	0.37913		1450
Synonymous	-0.392	166	160	1.04	0.00000996	1294
Loss of Function	4.31	10	39.1	0.256	0.00000200	461

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000477	0.000475
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000222	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000222	0.000217
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves peptide bonds on the C-terminal side of prolyl residues within peptides that are up to approximately 30 amino acids long.
• Pathway: Renin-angiotensin system - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.389

Intolerance Scores

• loftool: 0.473
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.0926
• hipred: Y
• hipred_score: 0.786
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.403

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prep
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;cytoplasm;cytosol;membrane
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;protein binding;serine-type peptidase activity;serine-type exopeptidase activity;oligopeptidase activity