APOC1

apolipoprotein C1, the group of Apolipoproteins

Basic information

Region (hg38): 19:44914247-44919349

Links

ENSG00000130208

∙ NCBI:341 ∙ OMIM:107710 ∙ HGNC:607 ∙ Uniprot:P02654 ∙ 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 APOC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOC1 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			3 clinvar	1 clinvar		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in APOC1

This is a list of pathogenic ClinVar variants found in the APOC1 region.

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

Position	Phenotype	Significance	ClinVar
19-44914898-C-T	not specified	Uncertain significance (Sep 16, 2021)	2365660
19-44914932-T-C	not specified	Uncertain significance (Feb 14, 2023)	2483847
19-44916219-G-A	not specified	Uncertain significance (Nov 22, 2022)	2371756
19-44919176-G-T	not specified	Likely benign (Dec 11, 2023)	3127992

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOC1	protein_coding	protein_coding	ENST00000588750	3	5103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.217	0.658	125686	0	34	125720	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0858	45	46.6	0.965	0.00000258	525
Missense in Polyphen		14	17.829	0.78523		223
Synonymous	0.178	18	19.0	0.948	9.40e-7	168
Loss of Function	1.07	1	2.99	0.334	1.26e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000544	0.000544
South Asian	0.000555	0.000555
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Inhibitor of lipoprotein binding to the low density lipoprotein (LDL) receptor, LDL receptor-related protein, and very low density lipoprotein (VLDL) receptor. Associates with high density lipoproteins (HDL) and the triacylglycerol-rich lipoproteins in the plasma and makes up about 10% of the protein of the VLDL and 2% of that of HDL. Appears to interfere directly with fatty acid uptake and is also the major plasma inhibitor of cholesteryl ester transfer protein (CETP). Binds free fatty acids and reduces their intracellular esterification. Modulates the interaction of APOE with beta-migrating VLDL and inhibits binding of beta-VLDL to the LDL receptor-related protein. {ECO:0000269|PubMed:17339654, ECO:0000303|PubMed:25160599}.;
Pathway: Cholesterol metabolism - Homo sapiens (human);Statin Pathway, Pharmacodynamics;Statin 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: 0.471

Intolerance Scores

loftool: 0.758
rvis_EVS: -0.05
rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

pHI: 0.0944
hipred: N
hipred_score: 0.146
ghis: 0.693

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Apoc1
Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name: apoc1
Affected structure: whole organism
Phenotype tag: abnormal
Phenotype quality: malformed

Gene ontology

Biological process: lipid metabolic process;triglyceride metabolic process;cholesterol metabolic process;positive regulation of cholesterol esterification;negative regulation of phosphatidylcholine catabolic process;negative regulation of very-low-density lipoprotein particle clearance;regulation of cholesterol transport;negative regulation of cholesterol transport;cholesterol efflux;phospholipid efflux;plasma lipoprotein particle remodeling;high-density lipoprotein particle remodeling;very-low-density lipoprotein particle assembly;chylomicron remnant clearance;very-low-density lipoprotein particle clearance;lipoprotein metabolic process;positive regulation of catalytic activity;negative regulation of fatty acid biosynthetic process;negative regulation of lipid metabolic process;negative regulation of receptor-mediated endocytosis;negative regulation of lipid catabolic process;negative regulation of lipoprotein lipase activity
Cellular component: extracellular region;endoplasmic reticulum;very-low-density lipoprotein particle;high-density lipoprotein particle;chylomicron
Molecular function: phospholipase inhibitor activity;fatty acid binding;phosphatidylcholine binding;lipase inhibitor activity;phosphatidylcholine-sterol O-acyltransferase activator activity