APOL2

apolipoprotein L2, the group of Apolipoproteins

Basic information

Region (hg38): 22:36226209-36239954

Links

ENSG00000128335NCBI:23780OMIM:607252HGNC:619Uniprot:Q9BQE5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APOL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL2 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
47
clinvar
3
clinvar
1
clinvar
51
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 47 3 1

Variants in APOL2

This is a list of pathogenic ClinVar variants found in the APOL2 region.

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

Position Type Phenotype Significance ClinVar
22-36227430-T-G not specified Uncertain significance (Dec 27, 2023)3128026
22-36227448-G-C not specified Uncertain significance (Dec 04, 2024)3418131
22-36227477-G-A not specified Uncertain significance (Sep 08, 2024)3418090
22-36227576-C-A not specified Uncertain significance (Mar 28, 2023)2569165
22-36227582-G-A not specified Uncertain significance (Dec 31, 2024)2340768
22-36227583-T-G not specified Uncertain significance (Apr 28, 2023)2541664
22-36227613-T-C not specified Uncertain significance (Feb 07, 2025)3886600
22-36227624-G-A not specified Uncertain significance (Aug 05, 2024)3418110
22-36227627-G-A not specified Uncertain significance (Jun 28, 2024)3418100
22-36227642-C-T not specified Likely benign (Sep 24, 2024)3418141
22-36227658-C-T not specified Uncertain significance (Nov 23, 2024)2352508
22-36227672-A-G not specified Uncertain significance (Apr 08, 2024)3308603
22-36227675-C-T not specified Uncertain significance (Aug 27, 2024)3418069
22-36227699-G-T not specified Uncertain significance (Aug 10, 2024)3418121
22-36227706-C-T not specified Uncertain significance (Jul 19, 2023)2612690
22-36227744-C-T not specified Uncertain significance (Sep 03, 2024)3418049
22-36227745-G-A not specified Uncertain significance (Oct 06, 2021)2356198
22-36227768-G-A not specified Uncertain significance (Sep 17, 2021)2251111
22-36227795-G-A not specified Uncertain significance (Dec 22, 2023)3128024
22-36227796-T-G not specified Uncertain significance (Dec 28, 2022)2210447
22-36227801-A-G not specified Uncertain significance (Nov 08, 2024)3418162
22-36227811-T-A not specified Uncertain significance (Jun 24, 2022)2216017
22-36227880-G-C not specified Likely benign (Nov 18, 2022)2327663
22-36227882-G-A not specified Uncertain significance (Aug 17, 2021)2245990
22-36227891-C-G not specified Uncertain significance (Feb 26, 2025)3886641

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
APOL2protein_codingprotein_codingENST00000249066 313745
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007310.5541256920501257420.000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7302171891.150.00001052187
Missense in Polyphen4951.5480.95057726
Synonymous-1.258874.31.190.00000403701
Loss of Function0.10733.210.9361.36e-736

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003290.000329
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001590.000158
Middle Eastern0.000.00
South Asian0.0007970.000784
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May affect the movement of lipids in the cytoplasm or allow the binding of lipids to organelles.;

Recessive Scores

pRec
0.0508

Intolerance Scores

loftool
0.761
rvis_EVS
0.2
rvis_percentile_EVS
67.3

Haploinsufficiency Scores

pHI
0.0267
hipred
N
hipred_score
0.112
ghis
0.443

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.148

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Apol8
Phenotype

Gene ontology

Biological process
lipid metabolic process;lipid transport;acute-phase response;multicellular organism development;cholesterol metabolic process;lipoprotein metabolic process;maternal process involved in female pregnancy
Cellular component
extracellular region;endoplasmic reticulum membrane;membrane
Molecular function
signaling receptor binding;high-density lipoprotein particle binding;lipid binding