APOC4-APOC2

APOC4-APOC2 readthrough (NMD candidate)

Basic information

Region (hg38): 19:44942238-44949565

Links

ENSG00000224916 ∙ NCBI:100533990 ∙ ∙ HGNC:44426 ∙ ∙ ∙ 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-APOC2 gene.

• not provided (42 variants)
• Cardiovascular phenotype (39 variants)
• Familial apolipoprotein C-II deficiency (36 variants)
• Inborn genetic diseases (10 variants)
• not specified (4 variants)
• Apolipoprotein c-ii variant (1 variants)
• APOLIPOPROTEIN C-II (WAKAYAMA) (1 variants)
• APOLIPOPROTEIN C-II (TORONTO) (1 variants)
• APOLIPOPROTEIN C-II (PARIS) (1 variants)
• APOLIPOPROTEIN C-II (PADOVA) (1 variants)
• APOLIPOPROTEIN C-II (BARI) (1 variants)
• APOLIPOPROTEIN C-II (ST. MICHAEL) (1 variants)
• APOLIPOPROTEIN C-II (AUCKLAND) (1 variants)
• APOLIPOPROTEIN C-II (SAN FRANCISCO) (1 variants)
• APOLIPOPROTEIN C-II (HAMBURG) (1 variants)
• APOLIPOPROTEIN C-II (AFRICAN) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOC4-APOC2 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				19		19
missense	2		24	8		34
nonsense	5	1				6
start loss						0
frameshift	5					5
inframe indel						0
splice donor/acceptor (+/-2bp)	1		2	1	1	5
splice region						0
non coding			11	12	10	33
Total	13	1	37	40	11

Highest pathogenic variant AF is 0.0000329

Variants in APOC4-APOC2

This is a list of pathogenic ClinVar variants found in the APOC4-APOC2 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)
19-44946027-T-G		Familial apolipoprotein C-II deficiency	Benign (Jan 13, 2018)
19-44946044-C-T		Familial apolipoprotein C-II deficiency	Uncertain significance (Jan 13, 2018)
19-44946051-G-C		Familial apolipoprotein C-II deficiency	Uncertain significance (Jan 13, 2018)
19-44946071-G-A		Familial apolipoprotein C-II deficiency	Uncertain significance (Jan 13, 2018)
19-44946083-A-G		Familial apolipoprotein C-II deficiency	Uncertain significance (Jan 31, 2022)
19-44948185-A-G			Benign (Aug 30, 2018)
19-44948277-T-G			Likely benign (Jan 16, 2021)
19-44948363-T-A		not specified	Benign (Aug 30, 2018)
19-44948390-C-G			Benign (Oct 17, 2018)
19-44948391-C-G			Likely benign (Dec 20, 2018)
19-44948399-T-G			Benign (Aug 30, 2018)
19-44948477-C-T		Familial apolipoprotein C-II deficiency • Cardiovascular phenotype • APOC2-related disorder	Benign/Likely benign (Mar 12, 2024)
19-44948479-A-G		APOLIPOPROTEIN C-II (PARIS) • Familial apolipoprotein C-II deficiency	Pathogenic (Dec 15, 1989)
19-44948482-G-C		Cardiovascular phenotype	Uncertain significance (May 30, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.394

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid metabolic process;lipid transport;positive regulation of catalytic activity
• Cellular component: chylomicron
• Molecular function: enzyme activator activity