APOL3

apolipoprotein L3, the group of Apolipoproteins

Basic information

Region (hg38): 22:36140328-36166177

Links

ENSG00000128284 ∙ NCBI:80833 ∙ OMIM:607253 ∙ HGNC:14868 ∙ Uniprot:O95236 ∙ 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 APOL3 gene.

• Inborn genetic diseases (17 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL3 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				1	1	2
missense			15	3	4	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	16	4	6

Variants in APOL3

This is a list of pathogenic ClinVar variants found in the APOL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-36141214-A-G		not specified	Uncertain significance (Nov 20, 2023)
22-36141225-C-T		not specified	Likely benign (Oct 26, 2022)
22-36141280-G-A		not specified	Uncertain significance (Dec 07, 2023)
22-36141397-G-A		not specified	Uncertain significance (Aug 12, 2021)
22-36141418-G-A		not specified	Uncertain significance (Jan 03, 2024)
22-36141431-A-C		not specified	Uncertain significance (Mar 29, 2022)
22-36141489-A-G		not specified	Uncertain significance (Sep 20, 2023)
22-36141522-C-T		not specified	Uncertain significance (Dec 14, 2022)
22-36141537-A-G		not specified	Uncertain significance (Aug 11, 2022)
22-36141592-T-A		not specified	Uncertain significance (Nov 18, 2022)
22-36141597-C-T		not specified	Likely benign (Jan 08, 2024)
22-36141675-G-A		not specified	Uncertain significance (Oct 12, 2022)
22-36141723-G-A		not specified	Uncertain significance (Mar 28, 2023)
22-36141727-C-T			Benign (Apr 09, 2018)
22-36141732-A-G		not specified	Uncertain significance (Jan 06, 2023)
22-36141735-C-T		not specified	Uncertain significance (Jun 18, 2021)
22-36141750-G-A			Benign (Apr 16, 2018)
22-36141764-C-T			Likely benign (Dec 31, 2019)
22-36141795-C-A		not specified	Uncertain significance (Dec 19, 2022)
22-36141889-C-T		not specified	Uncertain significance (Sep 29, 2023)
22-36142005-G-A			Benign (Dec 31, 2019)
22-36142014-G-A		not specified	Uncertain significance (Jan 30, 2024)
22-36142057-C-G		not specified	Uncertain significance (Feb 13, 2024)
22-36145519-T-C			Benign (May 17, 2018)
22-36145569-T-C		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOL3	protein_coding	protein_coding	ENST00000349314	3	25854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000436	0.434	122099	436	3203	125738	0.0146

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0414	228	226	1.01	0.0000123	2569
Missense in Polyphen		56	68.556	0.81685		801
Synonymous	-0.879	101	90.4	1.12	0.00000494	857
Loss of Function	0.0582	5	5.14	0.972	2.17e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.231	0.229
Ashkenazi Jewish	0.00546	0.00547
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000652	0.000519
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.00750	0.00752

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.78

Haploinsufficiency Scores

• pHI: 0.0436
• hipred: N
• hipred_score: 0.112
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0738

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid transport;inflammatory response;lipoprotein metabolic process;positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: extracellular region;cytoplasm;membrane
• Molecular function: lipid transporter activity;lipid binding