APOL4

protein-coding

apolipoprotein L4, the group of Apolipoproteins

Gene summary

This gene encodes a member of the apolipoprotein L family. The encoded protein may play a role in lipid exchange and transport throughout the body, as well as in reverse cholesterol transport from peripheral cells to the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2020]

MANE transcript

NM_001386885.1

Inheritance

—

ClinVar variants

U:12B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr22:36,189,124-36,204,840

External References & Databases

Ensembl (ENSG00000100336)

Transcript & Mutation Effects

hg38 • Region Span ~15.7 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 APOL4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 11

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001386885.1. 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			12 clinvar	3 clinvar		15
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	12	4	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001386885.1	RefSeq	NP_001373814.1	4	MANE Select
ENST00000683024.1	Ensembl	ENSP00000507418.1	4	MANE Select
NM_030643.4	RefSeq	NP_085146.2	4	Standard
NM_145660.2	RefSeq	NP_663693.1	4	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

molecular_function
lipid binding

Cellular Component

cellular_component
extracellular space
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000352371
Coding exons: 5
Length: 15715
Individuals with no LoFs: 125433
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125457
p: 0.0000957

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0220	189	188	1.00	0.0000100	2243
Missense (PolyPhen)		35	49.72	0.70394		629
Synonymous	-1.35	87	72.4	1.20	0.00000389	717
Loss of Function	0.567	5	6.57	0.761	2.78e-7	78

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in lipid exchange and transport throughout the body. May participate in reverse cholesterol transport from peripheral cells to the liver (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0795

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.121

Gene Damage Prediction

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