LSR

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

Basic information

Region (hg38): 19:35248330-35267964

Links

ENSG00000105699NCBI:51599OMIM:616582HGNC:29572Uniprot:Q86X29AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
14
clinvar
6
clinvar
20
missense
84
clinvar
7
clinvar
4
clinvar
95
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
inframe indel
1
clinvar
1
clinvar
1
clinvar
3
splice donor/acceptor (+/-2bp)
0
splice region
2
1
1
4
non coding
8
clinvar
4
clinvar
12
Total 0 0 86 31 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
19-35248890-C-G not specified Uncertain significance (Oct 20, 2024)3540978
19-35248900-G-A not specified Likely benign (Feb 20, 2025)3868890
19-35248915-G-C Uncertain significance (Mar 12, 2024)3687718
19-35248945-TC-T Likely benign (Nov 05, 2024)2861251
19-35248949-G-A Uncertain significance (Nov 11, 2024)3669462
19-35248960-G-A not specified Uncertain significance (Dec 11, 2024)3868884
19-35248967-G-C not specified Uncertain significance (Jun 06, 2023)2557831
19-35248970-C-A not specified Uncertain significance (Dec 16, 2024)3868888
19-35249008-G-A not specified Uncertain significance (Jan 16, 2024)1911637
19-35249012-A-G Likely benign (Mar 13, 2023)2068230
19-35249030-T-A Uncertain significance (Jan 19, 2023)2878536
19-35249038-G-C Benign (Jan 06, 2025)2126199
19-35249039-G-A not specified Uncertain significance (Mar 03, 2025)3868885
19-35249039-GC-AA Uncertain significance (Dec 16, 2024)1909228
19-35249041-G-A Uncertain significance (Dec 07, 2023)2863333
19-35249047-T-G not specified Uncertain significance (Feb 01, 2023)2473805
19-35249054-G-A not specified Uncertain significance (Mar 21, 2023)2540202
19-35249055-G-T Likely benign (May 01, 2023)2649715
19-35249056-C-T Benign/Likely benign (Mar 01, 2025)3667888
19-35249065-C-T not specified Uncertain significance (Apr 24, 2023)2407782
19-35249078-C-G not specified Uncertain significance (Jan 26, 2022)2220346
19-35249088-C-T Likely benign (Jan 23, 2025)2796679
19-35249090-C-A Uncertain significance (Oct 14, 2022)2070372
19-35249095-G-A not specified Uncertain significance (Nov 06, 2023)3121350
19-35249095-G-T Likely benign (Aug 21, 2024)2746821

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LSRprotein_codingprotein_codingENST00000361790 1019635
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.52e-80.9711257080401257480.000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6294444081.090.00002444125
Missense in Polyphen148162.520.910641598
Synonymous-0.1421811791.010.00001131355
Loss of Function2.091627.90.5730.00000140301

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002130.000212
Ashkenazi Jewish0.000.00
East Asian0.0001650.000163
Finnish0.000.00
European (Non-Finnish)0.0002520.000246
Middle Eastern0.0001650.000163
South Asian0.00009840.0000980
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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
Molecular function