PLTP
Basic information
Region (hg38): 20:45898621-45912155
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (118 variants)
- not_specified (64 variants)
- PLTP-related_disorder (6 variants)
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. These statistics are base on transcript: NM_000006227.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 28 | 34 | ||||
missense | 104 | 110 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 0 | 108 | 32 | 8 |
GnomAD
Source:
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:
- 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