APOL5

apolipoprotein L5, the group of Apolipoproteins

Basic information

Region (hg38): 22:35717872-35729483

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.

• not_specified (65 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. These statistics are base on transcript: NM_000030642.1. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			60	5	1	66
nonsense						0
start loss						0
frameshift					1	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	60	5	2

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