APOF

apolipoprotein F, the group of Apolipoproteins

Basic information

Region (hg38): 12:56360567-56362857

Links

ENSG00000175336 ∙ NCBI:319 ∙ OMIM:107760 ∙ HGNC:615 ∙ Uniprot:Q13790 ∙ 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 APOF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOF gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in APOF

This is a list of pathogenic ClinVar variants found in the APOF region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-56361233-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-56361245-C-A		not specified	Uncertain significance (Oct 06, 2021)
12-56361410-C-T		not specified	Uncertain significance (Dec 06, 2023)
12-56361452-C-T		not specified	Uncertain significance (Apr 01, 2024)
12-56361456-C-A		not specified	Uncertain significance (Jan 03, 2022)
12-56361508-G-A		not specified	Uncertain significance (Feb 10, 2023)
12-56361519-C-G		not specified	Uncertain significance (Dec 15, 2021)
12-56361583-C-A		not specified	Uncertain significance (Apr 06, 2024)
12-56361617-T-C		not specified	Uncertain significance (Mar 01, 2024)
12-56361656-G-C		not specified	Uncertain significance (Feb 15, 2023)
12-56361710-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-56361737-G-C		not specified	Uncertain significance (Oct 10, 2023)
12-56361764-C-T		not specified	Uncertain significance (Apr 07, 2022)
12-56361792-C-A		not specified	Uncertain significance (Nov 02, 2023)
12-56361809-C-T		not specified	Uncertain significance (Feb 15, 2023)
12-56361843-C-A		not specified	Uncertain significance (Mar 26, 2024)
12-56361865-T-C		not specified	Uncertain significance (Oct 03, 2023)
12-56361868-C-T			Benign (Oct 17, 2017)
12-56361890-C-T		not specified	Uncertain significance (Oct 25, 2022)
12-56362111-T-A		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOF	protein_coding	protein_coding	ENST00000398189	2	2255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.840	124547	0	89	124636	0.000357

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.355	161	174	0.924	0.00000869	2074
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000417
Ashkenazi Jewish	0.000697	0.000696
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000621	0.000620
Middle Eastern	0.000167	0.000167
South Asian	0.0000658	0.0000654
Other	0.00	0.00

dbNSFP

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}.
• Pathway: LDL remodeling;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.752
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apof
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: lipid metabolic process;lipid transport;cholesterol metabolic process
• Cellular component: extracellular space;low-density lipoprotein particle;high-density lipoprotein particle
• Molecular function: signaling receptor binding;lipid transporter activity;cholesterol binding