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.

• not_provided (113 variants)
• not_specified (107 variants)
• Progressive_familial_intrahepatic_cholestasis (1 variants)
• Progressive_familial_intrahepatic_cholestasis_type_1 (1 variants)

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. These statistics are base on transcript: NM_000205834.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	28	6	35
missense		1	128	8	2	139
nonsense			2			2
start loss			1			1
frameshift			1			1
splice donor/acceptor (+/-2bp)		1	3			4
Total	0	2	136	36	8

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
		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

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

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