CETP

cholesteryl ester transfer protein, the group of BPI fold containing

Basic information

Region (hg38): 16:56961922-56983845

Links

ENSG00000087237 ∙ NCBI:1071 ∙ OMIM:118470 ∙ HGNC:1869 ∙ Uniprot:P11597 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cholesterol-ester transfer protein deficiency (Strong), mode of inheritance: AD
• cholesterol-ester transfer protein deficiency (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperalphalipoproteinemia 1	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular	6738363; 3937535; 3867663; 2215607; 8675707; 12080388; 12499392; 15840744; 16049032; 17952847; 18354102; 19060911; 19428034; 20686565; 21354572; 21488146; 22122993; 22339301

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CETP gene.

• not provided (161 variants)
• Hyperalphalipoproteinemia 1 (65 variants)
• Inborn genetic diseases (28 variants)
• not specified (2 variants)
• Coronary artery disorder (2 variants)
• Abnormal circulating lipid concentration (1 variants)
• High density lipoprotein cholesterol level quantitative trait locus 10 (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CETP 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			1	22	8	31
missense			57	16	5	78
nonsense	1	2	2			5
start loss						0
frameshift		2	5			7
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1	1			3
splice region			7	2	2	11
non coding			1	28	42	71
Total	2	5	67	66	55

Highest pathogenic variant AF is 0.0000657

Variants in CETP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-56961996-T-A			Likely benign (Jan 05, 2024)
16-56962002-C-T		Hyperalphalipoproteinemia 1	Uncertain significance (-)
16-56962022-G-T		not specified	Uncertain significance (Jun 30, 2022)
16-56962023-C-G		Hyperalphalipoproteinemia 1	Benign (Jan 24, 2024)
16-56962023-C-T		not specified	Likely benign (Jun 30, 2022)
16-56962045-C-A		Hyperalphalipoproteinemia 1 • CETP-related disorder	Benign/Likely benign (Jan 29, 2024)
16-56962047-C-T			Uncertain significance (Jan 16, 2024)
16-56962052-G-A		not specified	Conflicting classifications of pathogenicity (Jun 06, 2023)
16-56962063-C-T		Hyperalphalipoproteinemia 1	Benign (Jan 12, 2018)
16-56962064-G-A			Uncertain significance (May 25, 2023)
16-56962068-G-A			Conflicting classifications of pathogenicity (Nov 01, 2023)
16-56962070-C-T			Uncertain significance (Oct 05, 2021)
16-56962071-G-A		Hyperalphalipoproteinemia 1	Uncertain significance (Aug 08, 2023)
16-56962087-C-T			Likely benign (Aug 14, 2023)
16-56962148-C-A			Likely benign (Mar 14, 2020)
16-56962192-C-A			Benign (Sep 17, 2018)
16-56962246-T-C			Benign (Aug 30, 2018)
16-56962299-G-A			Benign (Aug 30, 2018)
16-56962367-C-T			Likely benign (Nov 07, 2018)
16-56962376-G-A		Coronary artery disorder	Benign (May 12, 2022)
16-56962733-GCC-G			Benign (Aug 30, 2018)
16-56962737-C-A			Benign (Aug 30, 2018)
16-56962795-G-T			Likely benign (Apr 01, 2019)
16-56963017-C-G			Uncertain significance (May 17, 2023)
16-56963051-C-T		Hyperalphalipoproteinemia 1	Likely pathogenic (Aug 25, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CETP	protein_coding	protein_coding	ENST00000200676	16	21996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-23	0.000152	125640	1	107	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.526	290	266	1.09	0.0000153	3240
Missense in Polyphen		56	62.346	0.89821		827
Synonymous	-0.735	125	115	1.09	0.00000768	962
Loss of Function	-0.612	33	29.4	1.12	0.00000166	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000489	0.000489
Finnish	0.00144	0.00143
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000489	0.000489
South Asian	0.000490	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the transfer of neutral lipids, including cholesteryl ester and triglyceride, among lipoprotein particles. Allows the net movement of cholesteryl ester from high density lipoproteins/HDL to triglyceride-rich very low density lipoproteins/VLDL, and the equimolar transport of triglyceride from VLDL to HDL (PubMed:3600759, PubMed:24293641). Regulates the reverse cholesterol transport, by which excess cholesterol is removed from peripheral tissues and returned to the liver for elimination (PubMed:17237796). {ECO:0000269|PubMed:24293641, ECO:0000303|PubMed:17237796, ECO:0000305|PubMed:3600759}.
• Disease: DISEASE: Hyperalphalipoproteinemia 1 (HALP1) [MIM:143470]: A condition characterized by high levels of high density lipoprotein (HDL) and increased HDL cholesterol levels. {ECO:0000269|PubMed:12091484, ECO:0000269|PubMed:2215607, ECO:0000269|PubMed:8408659}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Cholesterol metabolism - Homo sapiens (human);Composition of Lipid Particles;Statin Pathway;LDL remodeling;HDL remodeling;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.370

Intolerance Scores

• loftool: 0.970
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.84

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.123
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.681

Gene Damage Prediction

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

Gene ontology

• Biological process: triglyceride metabolic process;lipid transport;cholesterol metabolic process;negative regulation of macrophage derived foam cell differentiation;regulation of cholesterol efflux;phospholipid transport;cholesterol transport;triglyceride transport;very-low-density lipoprotein particle remodeling;low-density lipoprotein particle remodeling;high-density lipoprotein particle remodeling;cholesterol homeostasis;reverse cholesterol transport;phosphatidylcholine metabolic process;lipid homeostasis;phospholipid homeostasis;triglyceride homeostasis
• Cellular component: extracellular region;extracellular space;vesicle;high-density lipoprotein particle;extracellular exosome
• Molecular function: lipid transporter activity;phospholipid transporter activity;lipid binding;cholesterol binding;cholesterol transporter activity;triglyceride binding;phosphatidylcholine binding