APOL2

protein-coding

apolipoprotein L2, 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. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_030882.4

Inheritance

ClinVar variants

U:76B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr22:36,226,209-36,239,954

External References & Databases

Ensembl (ENSG00000128335)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to APOL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030882.4. 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				1 clinvar		1
missense			73 clinvar	7 clinvar	1 clinvar	81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	76	8	1	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030882.4	RefSeq	NP_112092.2	3	MANE Select
ENST00000358502.10	Ensembl	ENSP00000351292.5	3	MANE Select
NM_145637.3	RefSeq	NP_663612.2	3	Standard
ENST00000249066.10	Ensembl	ENSP00000249066.6	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid metabolic process
lipid transport
acute-phase response
multicellular organism development
cholesterol metabolic process

Molecular Function

signaling receptor binding
high-density lipoprotein particle binding
lipid binding

Cellular Component

extracellular region
endoplasmic reticulum membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000249066
Coding exons: 3
Length: 13745
Individuals with no LoFs: 125692
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125742
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.730	217	189	1.15	0.0000105	2187
Missense (PolyPhen)		49	51.548	0.95057		726
Synonymous	-1.25	88	74.3	1.19	0.00000403	701
Loss of Function	0.107	3	3.21	0.936	1.36e-7	36

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00080	0.00078	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0508

Intolerance Scores

LoFtool: 0.761
RVIS EVS: 0.2
RVIS percentile EVS: 67.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.148

Gene Damage Prediction

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