APOC4

apolipoprotein C4, the group of Apolipoproteins

Basic information

Region (hg38): 19:44942236-44945496

Links

ENSG00000267467 ∙ NCBI:346 ∙ OMIM:600745 ∙ HGNC:611 ∙ Uniprot:P55056 ∙ 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 APOC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOC4 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in APOC4

This is a list of pathogenic ClinVar variants found in the APOC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44942284-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-44942287-C-T		not specified	Uncertain significance (Apr 23, 2024)
19-44942345-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-44942347-A-T		not specified	Uncertain significance (Aug 17, 2022)
19-44944809-G-A		not specified	Likely benign (Jun 05, 2024)
19-44944862-A-G		not specified	Uncertain significance (May 11, 2022)
19-44945156-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-44945166-T-C		not specified	Uncertain significance (Nov 07, 2022)
19-44945183-G-C		not specified	Uncertain significance (Apr 17, 2024)
19-44945228-G-A		not specified	Likely benign (Mar 29, 2023)
19-44945274-G-C		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOC4	protein_coding	protein_coding	ENST00000419266	3	7326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.89e-8	0.0494	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	62	67.9	0.914	0.00000352	815
Missense in Polyphen		13	21.879	0.59417		279
Synonymous	-0.676	35	30.3	1.16	0.00000171	249
Loss of Function	-1.20	9	5.87	1.53	2.51e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in lipoprotein metabolism.
• Pathway: VLDL assembly;Plasma lipoprotein assembly;VLDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.296

Intolerance Scores

• loftool: 0.592
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0800

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apoc4
• Phenotype: hematopoietic system phenotype; immune system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid metabolic process;lipid transport;positive regulation of sequestering of triglyceride;very-low-density lipoprotein particle assembly;very-low-density lipoprotein particle clearance;triglyceride homeostasis
• Cellular component: extracellular region;very-low-density lipoprotein particle;high-density lipoprotein particle
• Molecular function: lipid transporter activity