LSR

lipolysis stimulated lipoprotein receptor, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:35248330-35267964

Links

ENSG00000105699 ∙ NCBI:51599 ∙ OMIM:616582 ∙ HGNC:29572 ∙ Uniprot:Q86X29 ∙ 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 LSR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSR 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				11	6	17
missense			72	6	4	82
nonsense			1			1
start loss						0
frameshift				1		1
inframe indel			1	1	1	3
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding				6	4	10
Total	0	0	74	25	15

Variants in LSR

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

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

Position	Type	Phenotype	Significance	ClinVar
19-35248945-TC-T			Likely benign (Jan 19, 2024)
19-35248967-G-C		not specified	Uncertain significance (Jun 06, 2023)
19-35249008-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-35249012-A-G			Likely benign (Mar 13, 2023)
19-35249030-T-A			Uncertain significance (Jan 19, 2023)
19-35249038-G-C			Benign (Nov 28, 2023)
19-35249039-GC-AA			Uncertain significance (Oct 13, 2022)
19-35249041-G-A			Uncertain significance (Dec 07, 2023)
19-35249047-T-G		not specified	Uncertain significance (Feb 01, 2023)
19-35249054-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-35249055-G-T			Likely benign (May 01, 2023)
19-35249065-C-T		not specified	Uncertain significance (Apr 24, 2023)
19-35249078-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-35249088-C-T			Likely benign (Jan 07, 2024)
19-35249090-C-A			Uncertain significance (Oct 14, 2022)
19-35249095-G-A		not specified	Uncertain significance (Nov 06, 2023)
19-35249095-G-T			Likely benign (Nov 27, 2023)
19-35249107-C-T			Uncertain significance (Nov 24, 2022)
19-35249120-C-A			Uncertain significance (Jul 03, 2023)
19-35249135-C-T			Likely benign (Nov 22, 2023)
19-35249143-G-C			Benign (Jan 14, 2024)
19-35250355-C-T			Benign/Likely benign (Jan 24, 2024)
19-35250359-G-A		not specified	Uncertain significance (Aug 08, 2022)
19-35250454-C-G		not specified	Uncertain significance (May 03, 2023)
19-35250458-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSR	protein_coding	protein_coding	ENST00000361790	10	19635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.52e-8	0.971	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.629	444	408	1.09	0.0000244	4125
Missense in Polyphen		148	162.52	0.91064		1598
Synonymous	-0.142	181	179	1.01	0.0000113	1355
Loss of Function	2.09	16	27.9	0.573	0.00000140	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000212
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000246
Middle Eastern	0.000165	0.000163
South Asian	0.0000984	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable role in the clearance of triglyceride-rich lipoprotein from blood. Binds chylomicrons, LDL and VLDL in presence of free fatty acids and allows their subsequent uptake in the cells (By similarity). {ECO:0000250}.
• Pathway: LDL clearance;VLDL clearance;Plasma lipoprotein clearance;Transport of small molecules;EGFR1;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.199

Intolerance Scores

• loftool: 0.922
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.89

Haploinsufficiency Scores

• pHI: 0.605
• hipred: N
• hipred_score: 0.146
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsr
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; liver/biliary 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: lsr
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: liver development;regulation of lipid metabolic process;establishment of blood-brain barrier;tricellular tight junction assembly
• Cellular component: plasma membrane;integral component of membrane;very-low-density lipoprotein particle;low-density lipoprotein particle;chylomicron;tricellular tight junction;extracellular exosome