APOL2

apolipoprotein L2, the group of Apolipoproteins

Basic information

Region (hg38): 22:36226209-36239954

Links

ENSG00000128335 ∙ NCBI:23780 ∙ OMIM:607252 ∙ HGNC:619 ∙ Uniprot:Q9BQE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	3	1	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)
22-36227448-G-C		not specified	Uncertain significance (Dec 04, 2024)
22-36227477-G-A		not specified	Uncertain significance (Sep 08, 2024)
22-36227576-C-A		not specified	Uncertain significance (Mar 28, 2023)
22-36227582-G-A		not specified	Uncertain significance (Dec 31, 2024)
22-36227583-T-G		not specified	Uncertain significance (Apr 28, 2023)
22-36227613-T-C		not specified	Uncertain significance (Feb 07, 2025)
22-36227624-G-A		not specified	Uncertain significance (Aug 05, 2024)
22-36227627-G-A		not specified	Uncertain significance (Jun 28, 2024)
22-36227642-C-T		not specified	Likely benign (Sep 24, 2024)
22-36227658-C-T		not specified	Uncertain significance (Nov 23, 2024)
22-36227672-A-G		not specified	Uncertain significance (Apr 08, 2024)
22-36227675-C-T		not specified	Uncertain significance (Aug 27, 2024)
22-36227699-G-T		not specified	Uncertain significance (Aug 10, 2024)
22-36227706-C-T		not specified	Uncertain significance (Jul 19, 2023)
22-36227744-C-T		not specified	Uncertain significance (Sep 03, 2024)
22-36227745-G-A		not specified	Uncertain significance (Oct 06, 2021)
22-36227768-G-A		not specified	Uncertain significance (Sep 17, 2021)
22-36227795-G-A		not specified	Uncertain significance (Dec 22, 2023)
22-36227796-T-G		not specified	Uncertain significance (Dec 28, 2022)
22-36227801-A-G		not specified	Uncertain significance (Nov 08, 2024)
22-36227811-T-A		not specified	Uncertain significance (Jun 24, 2022)
22-36227880-G-C		not specified	Likely benign (Nov 18, 2022)
22-36227882-G-A		not specified	Uncertain significance (Aug 17, 2021)
22-36227891-C-G		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOL2	protein_coding	protein_coding	ENST00000249066	3	13745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00731	0.554	125692	0	50	125742	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.730	217	189	1.15	0.0000105	2187
Missense in Polyphen		49	51.548	0.95057		726
Synonymous	-1.25	88	74.3	1.19	0.00000403	701
Loss of Function	0.107	3	3.21	0.936	1.36e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00	0.00
South Asian	0.000797	0.000784
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Apol8

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