GeneBe

APOL1

apolipoprotein L1, the group of Apolipoproteins

Basic information

Region (hg38): 22:36253071-36267530

Previous symbols: [ "APOL" ]

Links

ENSG00000100342 ∙ NCBI:8542 ∙ OMIM:603743 ∙ HGNC:618 ∙ Uniprot:O14791 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • focal segmental glomerulosclerosis 4, susceptibility to (Strong), mode of inheritance: AR
  • focal segmental glomerulosclerosis 4, susceptibility to (Definitive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APOL1 gene.

  • not_provided (98 variants)
  • not_specified (59 variants)
  • Focal_segmental_glomerulosclerosis_4,_susceptibility_to (25 variants)
  • APOL1-related_disorder (14 variants)
  • Focal_segmental_glomerulosclerosis (3 variants)
  • Hyalinosis,_Segmental_Glomerular (3 variants)
  • Nephrotic_range_proteinuria (3 variants)
  • Glomerulonephritis (2 variants)
  • Steroid-resistant_nephrotic_syndrome (2 variants)
  • APOL1-associated_kidney_disease (2 variants)
  • Sickled_erythrocytes (2 variants)
  • Proteinuria (2 variants)
  • Corticosteroids_response (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003661.4. 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.

EffectPLPVUSLBBSum
synonymous
31
clinvar
1
clinvar
 32
missense
1
clinvar
79
clinvar
12
clinvar
6
clinvar
 98
nonsense
2
clinvar
 2
start loss
0
frameshift
1
clinvar
1
clinvar
 2
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 1 83 43 8

Highest pathogenic variant AF is 0.0114035

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
APOL1protein_codingprotein_codingENST00000319136 614521
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000005140.2541257210271257480.000107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5832592341.110.00001262701
Missense in Polyphen7057.4221.219745
Synonymous-0.95210492.41.130.00000539816
Loss of Function-0.023687.931.013.36e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.0004960.000496
East Asian0.0003260.000326
Finnish0.00004620.0000462
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.0003260.000326
South Asian0.0001960.000196
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in lipid exchange and transport throughout the body. May participate in reverse cholesterol transport from peripheral cells to the liver.;
Disease
DISEASE: Focal segmental glomerulosclerosis 4 (FSGS4) [MIM:612551]: A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and progressive decline in renal function. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation. {ECO:0000269|PubMed:20635188, ECO:0000269|PubMed:20647424}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
African trypanosomiasis - Homo sapiens (human);Vesicle-mediated transport;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Scavenging of heme from plasma;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Intolerance Scores

loftool
0.976
rvis_EVS
1.45
rvis_percentile_EVS
95.12

Haploinsufficiency Scores

pHI
0.0163
hipred
N
hipred_score
0.112
ghis
0.390

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.417

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Zebrafish Information Network

Gene name
apol1
Affected structure
podocyte
Phenotype tag
abnormal
Phenotype quality
disorganized

Gene ontology

Biological process
lipid transport;receptor-mediated endocytosis;cholesterol metabolic process;cytolysis;killing of cells of other organism;lipoprotein metabolic process;post-translational protein modification;cellular protein metabolic process;innate immune response;chloride transmembrane transport
Cellular component
extracellular region;extracellular space;endoplasmic reticulum lumen;intrinsic component of membrane;very-low-density lipoprotein particle;high-density lipoprotein particle;blood microparticle
Molecular function
chloride channel activity;protein binding;lipid binding