PLTP

phospholipid transfer protein, the group of BPI fold containing

Basic information

Region (hg38): 20:45898621-45912155

Links

ENSG00000100979 ∙ NCBI:5360 ∙ OMIM:172425 ∙ HGNC:9093 ∙ Uniprot:P55058 ∙ 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 PLTP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLTP 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				21	6	27
missense			67	4	2	73
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			4	4	1	9
non coding			2	10	3	15
Total	0	0	72	35	11

Variants in PLTP

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

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

Position	Type	Phenotype	Significance	ClinVar
20-45898716-T-A		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jan 12, 2018)
20-45898770-G-A		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jan 13, 2018)
20-45898965-G-A			Likely benign (Apr 07, 2022)
20-45898977-C-T			Likely benign (Oct 12, 2021)
20-45898990-G-C			Uncertain significance (May 07, 2021)
20-45898998-GTTC-G			Uncertain significance (Jul 03, 2023)
20-45899008-A-G		not specified	Uncertain significance (Jan 17, 2024)
20-45899081-G-C			Likely benign (Oct 18, 2023)
20-45899467-G-A			Uncertain significance (Oct 13, 2023)
20-45899471-C-T			Likely benign (Jan 28, 2022)
20-45899477-C-G			Benign (Jan 24, 2024)
20-45899478-A-G			Uncertain significance (Dec 09, 2021)
20-45899487-A-C		not specified	Uncertain significance (Aug 12, 2021)
20-45899514-A-T		not specified	Uncertain significance (Nov 10, 2022)
20-45899526-C-T			Uncertain significance (Aug 07, 2023)
20-45899538-T-G		not specified	Uncertain significance (Sep 30, 2022)
20-45899545-G-T		PLTP-related disorder	Likely benign (Feb 08, 2023)
20-45899640-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-45899640-CC-TG			Uncertain significance (Dec 23, 2023)
20-45899645-A-G			Uncertain significance (Aug 23, 2022)
20-45899660-T-A			Uncertain significance (Sep 08, 2023)
20-45899679-G-T		not specified	Uncertain significance (Mar 31, 2023)
20-45899689-G-C			Likely benign (Jan 18, 2024)
20-45899693-G-A			Likely benign (Apr 08, 2021)
20-45899703-G-A			Benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLTP	protein_coding	protein_coding	ENST00000477313	15	13396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.00e-9	0.741	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0155	291	290	1.00	0.0000190	3170
Missense in Polyphen		99	109.14	0.90713		1311
Synonymous	-0.499	126	119	1.06	0.00000728	1043
Loss of Function	1.41	16	23.4	0.685	0.00000111	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000359	0.000359
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitates the transfer of a spectrum of different lipid molecules, including diacylglycerol, phosphatidic acid, sphingomyelin, phosphatidylcholine, phosphatidylglycerol, cerebroside and phosphatidyl ethanolamine. Essential for the transfer of excess surface lipids from triglyceride-rich lipoproteins to HDL, thereby facilitating the formation of smaller lipoprotein remnants, contributing to the formation of LDL, and assisting in the maturation of HDL particles. PLTP also plays a key role in the uptake of cholesterol from peripheral cells and tissues that is subsequently transported to the liver for degradation and excretion. Two distinct forms of PLTP exist in plasma: an active form that can transfer PC from phospholipid vesicles to high-density lipoproteins (HDL), and an inactive form that lacks this capability.
• Pathway: Cholesterol metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Statin Pathway, Pharmacodynamics;PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;PPAR signaling pathway;Statin Pathway;HDL remodeling;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.955
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.363
• hipred: Y
• hipred_score: 0.610
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.717

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pltp
• Phenotype: reproductive system phenotype; vision/eye phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid metabolic process;lipid transport;vitamin E biosynthetic process;positive regulation of cholesterol efflux;phospholipid transport;flagellated sperm motility;high-density lipoprotein particle remodeling;ceramide transport
• Cellular component: extracellular region;extracellular space;high-density lipoprotein particle
• Molecular function: lipid transporter activity;phospholipid transporter activity;phosphatidylethanolamine binding;phosphatidylcholine transporter activity;diacylglycerol binding;phosphatidylcholine binding;ceramide transporter activity;phosphatidic acid binding;ceramide binding;phosphatidylglycerol binding;phosphatidylethanolamine transporter activity;phosphatidic acid transporter activity