APOL5

apolipoprotein L5, the group of Apolipoproteins

Basic information

Region (hg38): 22:35717871-35729483

Links

ENSG00000128313 ∙ NCBI:80831 ∙ OMIM:607255 ∙ HGNC:14869 ∙ Uniprot:Q9BWW9 ∙ 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 APOL5 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL5 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			23	3	1	27
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	2

Variants in APOL5

This is a list of pathogenic ClinVar variants found in the APOL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-35717882-G-C		not specified	Uncertain significance (Jun 27, 2022)
22-35717909-G-A		not specified	Uncertain significance (Apr 25, 2023)
22-35720601-G-A		not specified	Uncertain significance (Mar 03, 2022)
22-35720615-G-A		not specified	Uncertain significance (Jul 06, 2021)
22-35720634-A-G		not specified	Uncertain significance (Apr 25, 2023)
22-35720634-A-T		not specified	Uncertain significance (May 23, 2023)
22-35726261-A-G		not specified	Likely benign (Jan 27, 2022)
22-35726283-G-A		not specified	Likely benign (Nov 17, 2023)
22-35726283-G-T		not specified	Uncertain significance (Mar 24, 2023)
22-35726299-T-A		not specified	Uncertain significance (Feb 06, 2023)
22-35726309-G-A			Benign (Sep 06, 2017)
22-35726319-G-A		not specified	Uncertain significance (Nov 03, 2023)
22-35726343-A-G		not specified	Uncertain significance (Feb 05, 2024)
22-35726373-T-G		not specified	Uncertain significance (Sep 22, 2023)
22-35726462-G-A		not specified	Likely benign (Nov 17, 2022)
22-35726468-C-T		not specified	Uncertain significance (Jan 07, 2022)
22-35726501-G-A		not specified	Uncertain significance (Jan 09, 2023)
22-35726572-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-35726646-G-A		not specified	Uncertain significance (Oct 05, 2021)
22-35726661-C-G		not specified	Uncertain significance (Aug 14, 2023)
22-35726679-G-A		not specified	Uncertain significance (Jun 01, 2023)
22-35726714-G-A		not specified	Uncertain significance (Jan 06, 2023)
22-35726744-G-A		not specified	Uncertain significance (Apr 22, 2022)
22-35726786-A-C		not specified	Uncertain significance (Jan 16, 2024)
22-35727042-C-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOL5	protein_coding	protein_coding	ENST00000249044	4	11612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.01e-7	0.689	125554	0	194	125748	0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.370	221	237	0.932	0.0000127	2792
Missense in Polyphen		40	43.787	0.91351		568
Synonymous	-0.523	99	92.6	1.07	0.00000527	900
Loss of Function	1.15	12	17.2	0.699	0.00000113	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00581	0.00582
Ashkenazi Jewish	0.00	0.00
East Asian	0.00142	0.00141
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000353	0.000352
Middle Eastern	0.00142	0.00141
South Asian	0.000327	0.000327
Other	0.000664	0.000652

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: 0.865
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.19

Haploinsufficiency Scores

• pHI: 0.0593
• hipred: N
• hipred_score: 0.112
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000717

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: lipid metabolic process;lipid transport;lipoprotein metabolic process
• Cellular component: cellular_component;extracellular region;cytoplasm
• Molecular function: high-density lipoprotein particle binding;lipid binding