APOF

protein-coding

apolipoprotein F, the group of Apolipoproteins

Gene summary

The product of this gene is one of the minor apolipoproteins found in plasma. This protein forms complexes with lipoproteins and may be involved in transport and/or esterification of cholesterol. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001638.4

Inheritance

—

ClinVar variants

U:43B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr12:56,360,568-56,362,857

External References & Databases

Ensembl (ENSG00000175336)

Transcript & Mutation Effects

hg38 • Region Span ~2.3 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 APOF variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001638.4. 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			42 clinvar	1 clinvar	1 clinvar	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	1	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001638.4	RefSeq	NP_001629.1	2	MANE Select
ENST00000398189.4	Ensembl	ENSP00000381250.3	2	MANE Select
ENST00000887741.1	Ensembl	ENSP00000557800.1	2	Standard
ENST00000887741.2	Ensembl	ENSP00000557800.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

LDL remodeling
Transport of small molecules
Plasma lipoprotein assembly, remodeling, and clearance
Plasma lipoprotein remodeling

Biological Process

lipid metabolic process
lipid transport
cholesterol metabolic process

Molecular Function

signaling receptor binding
lipid transporter activity
cholesterol binding

Cellular Component

extracellular space
low-density lipoprotein particle
high-density lipoprotein particle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398189
Coding exons: 2
Length: 2255
Individuals with no LoFs: 124547
Homozygous LoFs: 0
Heterozygous LoFs: 89
Defined: 124636
p: 0.000357

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.355	161	174	0.924	0.00000869	2074
Missense (PolyPhen)		40	48.175	0.83031		589
Synonymous	-0.262	73	70.2	1.04	0.00000355	697
Loss of Function	1.16	4	7.42	0.539	3.83e-7	83

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00039	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00070	0.00070	rare
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00062	0.00062	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Minor apolipoprotein that associates with LDL. Inhibits cholesteryl ester transfer protein (CETP) activity and appears to be an important regulator of cholesterol transport. Also associates to a lesser degree with VLDL, Apo-AI and Apo-AII. {ECO:0000269|PubMed:9880564}.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.752
RVIS EVS: 0.73
RVIS percentile EVS: 86.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.861

Gene Damage Prediction

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