LRP2BP

LRP2 binding protein

Basic information

Region (hg38): 4:185363872-185395924

Links

ENSG00000109771 ∙ NCBI:55805 ∙ OMIM:619020 ∙ HGNC:25434 ∙ Uniprot:Q9P2M1 ∙ 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 LRP2BP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP2BP 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in LRP2BP

This is a list of pathogenic ClinVar variants found in the LRP2BP region.

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

Position	Type	Phenotype	Significance	ClinVar
4-185367227-C-T		not specified	Uncertain significance (May 01, 2022)
4-185367245-C-T		not specified	Uncertain significance (Dec 11, 2023)
4-185370741-C-T		not specified	Likely benign (Jul 12, 2022)
4-185370805-G-C		not specified	Uncertain significance (Dec 01, 2022)
4-185372859-T-C		not specified	Uncertain significance (Nov 14, 2023)
4-185372911-C-T		not specified	Uncertain significance (Jun 21, 2021)
4-185372920-C-T		not specified	Uncertain significance (Dec 13, 2021)
4-185372941-G-A		not specified	Uncertain significance (Jun 24, 2022)
4-185372960-G-C		not specified	Uncertain significance (Jun 14, 2023)
4-185372979-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-185372979-G-T		not specified	Uncertain significance (Dec 27, 2023)
4-185373016-G-A		not specified	Uncertain significance (Sep 09, 2021)
4-185374325-G-C		not specified	Uncertain significance (Dec 15, 2022)
4-185374340-C-T		not specified	Uncertain significance (Feb 10, 2023)
4-185374404-G-T		not specified	Uncertain significance (Mar 28, 2023)
4-185375651-C-A		not specified	Uncertain significance (Feb 02, 2022)
4-185375684-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-185376961-A-C		not specified	Likely benign (Jan 04, 2024)
4-185378174-T-C		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP2BP	protein_coding	protein_coding	ENST00000328559	8	32022

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000235	0.913	125648	0	100	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	176	195	0.902	0.0000106	2272
Missense in Polyphen		66	68.169	0.96818		765
Synonymous	1.11	64	76.3	0.839	0.00000467	626
Loss of Function	1.67	12	20.1	0.598	0.00000104	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000163	0.000163
South Asian	0.00114	0.00114
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as an adapter that regulates LRP2 function.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.880
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.535
• hipred: N
• hipred_score: 0.197
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrp2bp

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding