LRP5L

LDL receptor related protein 5 like (pseudogene)

Basic information

Region (hg38): 22:25351612-25405274

Links

ENSG00000100068 ∙ NCBI:91355 ∙ ∙ HGNC:25323 ∙ Uniprot:A4QPB2 ∙ 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 LRP5L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP5L 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP5L	protein_coding	protein_coding	ENST00000402859	4	53960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-11	0.0168	125468	2	257	125727	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.668	187	163	1.15	0.0000105	1652
Missense in Polyphen		64	55.102	1.1615		565
Synonymous	-1.73	89	70.6	1.26	0.00000521	495
Loss of Function	-0.851	14	11.0	1.28	5.59e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0129	0.0128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000202
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.106
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.8

Haploinsufficiency Scores

• pHI: 0.0920
• hipred: N
• hipred_score: 0.112
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Gene ontology

• Biological process: gastrulation with mouth forming second;osteoblast development;anterior/posterior pattern specification;cholesterol homeostasis;positive regulation of transcription by RNA polymerase II;bone remodeling;bone marrow development;canonical Wnt signaling pathway;bone morphogenesis;branching involved in mammary gland duct morphogenesis;adipose tissue development;regulation of insulin secretion involved in cellular response to glucose stimulus;retinal blood vessel morphogenesis
• Cellular component: plasma membrane;receptor complex
• Molecular function: Wnt-protein binding;Wnt-activated receptor activity