APOL5

protein-coding

apolipoprotein L5, the group of Apolipoproteins

Gene summary

This gene is a member of the apolipoprotein L gene family. The encoded protein is found in the cytoplasm, where it may affect the movement of lipids or allow the binding of lipids to organelles. [provided by RefSeq, Jul 2008]

MANE transcript

NM_030642.1

Inheritance

—

ClinVar variants

U:70B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr22:35,717,872-35,729,483

External References & Databases

Ensembl (ENSG00000128313)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to APOL5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030642.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			69 clinvar	6 clinvar	1 clinvar	76
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	70	6	2	78

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030642.1	RefSeq	NP_085145.1	4	MANE Select
ENST00000249044.2	Ensembl	ENSP00000249044.2	4	MANE Select
XM_006724321.5	RefSeq	XP_006724384.1	4	Standard
XM_017028945.3	RefSeq	XP_016884434.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid metabolic process
lipid transport
lipoprotein metabolic process

Molecular Function

high-density lipoprotein particle binding
lipid binding

Cellular Component

cellular_component
extracellular region
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000249044
Coding exons: 4
Length: 11612
Individuals with no LoFs: 125554
Homozygous LoFs: 0
Heterozygous LoFs: 194
Defined: 125748
p: 0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.370	221	237	0.932	0.0000127	2792
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0047	0.0047	notable
Latino/Admixed American	0.0011	0.0010	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0014	0.0014	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00033	0.00033	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0000717

Gene Damage Prediction

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