PRELP

proline and arginine rich end leucine rich repeat protein, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 1:203475805-203491352

Links

ENSG00000188783 ∙ NCBI:5549 ∙ OMIM:601914 ∙ HGNC:9357 ∙ Uniprot:P51888 ∙ 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 PRELP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRELP 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	2

Variants in PRELP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-203483218-C-T		not specified	Uncertain significance (Jul 08, 2022)
1-203483227-G-A		not specified	Uncertain significance (Jul 30, 2023)
1-203483269-G-A		not specified	Likely benign (Dec 22, 2023)
1-203483289-A-C		not specified	Uncertain significance (Sep 17, 2021)
1-203483293-A-G		not specified	Uncertain significance (Jun 11, 2021)
1-203483311-A-C		not specified	Uncertain significance (Sep 17, 2021)
1-203483405-C-T		not specified	Uncertain significance (Jun 07, 2023)
1-203483426-C-G		not specified	Uncertain significance (May 03, 2023)
1-203483458-C-T		not specified	Uncertain significance (Mar 21, 2022)
1-203483492-G-T		not specified	Uncertain significance (Mar 17, 2023)
1-203483636-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-203483687-C-A		not specified	Uncertain significance (Oct 13, 2023)
1-203483696-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-203483772-C-A		not specified	Uncertain significance (Dec 19, 2022)
1-203483796-C-A		not specified	Uncertain significance (Dec 28, 2023)
1-203483815-G-A		not specified	Uncertain significance (Dec 07, 2022)
1-203483868-G-A			Likely benign (May 01, 2022)
1-203483895-G-A			Benign (Jan 30, 2018)
1-203483899-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-203483962-G-A		PRELP-related osteosclerosis	Uncertain significance (Mar 19, 2018)
1-203483995-A-G		not specified	Uncertain significance (May 21, 2024)
1-203483998-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-203484040-A-G		not specified	Uncertain significance (Dec 06, 2023)
1-203486710-C-A			Benign (Jan 30, 2018)
1-203486722-G-C		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRELP	protein_coding	protein_coding	ENST00000343110	2	15525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000471	0.670	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.741	193	224	0.861	0.0000139	2498
Missense in Polyphen		64	77.169	0.82935		904
Synonymous	-1.22	119	103	1.15	0.00000677	813
Loss of Function	0.899	8	11.3	0.711	8.51e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000338	0.000333
Ashkenazi Jewish	0.000109	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000125	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.0000677	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May anchor basement membranes to the underlying connective tissue. {ECO:0000250}.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.58

Haploinsufficiency Scores

• pHI: 0.724
• hipred: N
• hipred_score: 0.335
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prelp
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: skeletal system development;cell aging;keratan sulfate biosynthetic process;keratan sulfate catabolic process
• Cellular component: extracellular region;Golgi lumen;extracellular matrix;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome;extracellular vesicle
• Molecular function: extracellular matrix structural constituent;heparin binding;extracellular matrix structural constituent conferring compression resistance