LIPI
Basic information
Region (hg38): 21:14108812-14210955
Links
Phenotypes
GenCC
Source:
- hypertriglyceridemia (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Hypertriglyceridemia, familial | AD | Cardiovascular | Surveillance and treatment for cholesterol and cardiovascular perturbations may decrease morbidity and mortality | Cardiovascular | 12719377 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (58 variants)
- Inborn genetic diseases (17 variants)
- Hypertriglyceridemia 1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPI 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 | 9 | |||||
missense | 31 | 42 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 1 | 2 | 2 | 5 | ||
non coding ? | 12 | |||||
Total | 0 | 0 | 37 | 11 | 19 |
Variants in LIPI
This is a list of pathogenic ClinVar variants found in the LIPI region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
21-14109008-T-G | Likely benign (Mar 23, 2021) | |||
21-14109044-G-T | Benign (Feb 01, 2024) | |||
21-14109045-T-A | Uncertain significance (Jan 15, 2022) | |||
21-14109087-AAG-A | Benign (Jul 17, 2023) | |||
21-14144627-C-T | Benign (Jan 31, 2024) | |||
21-14144655-A-A | Benign (Feb 01, 2024) | |||
21-14144707-T-C | Uncertain significance (Nov 14, 2022) | |||
21-14144714-A-G | Benign (Sep 19, 2022) | |||
21-14144736-A-C | not specified | Uncertain significance (Aug 17, 2022) | ||
21-14144737-A-C | Uncertain significance (Oct 27, 2022) | |||
21-14144819-C-T | Likely benign (Nov 05, 2022) | |||
21-14152595-T-C | not specified | Likely benign (Mar 22, 2022) | ||
21-14152600-C-T | Benign (Jan 31, 2024) | |||
21-14152617-T-G | Uncertain significance (Oct 07, 2021) | |||
21-14152629-C-T | Benign (Mar 29, 2023) | |||
21-14152645-G-T | Uncertain significance (Sep 04, 2023) | |||
21-14152657-A-C | Uncertain significance (Jun 16, 2023) | |||
21-14152661-T-G | not specified | Uncertain significance (Jan 08, 2024) | ||
21-14152684-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
21-14152687-A-G | Uncertain significance (Jan 18, 2023) | |||
21-14163406-G-A | Benign (Jan 26, 2024) | |||
21-14163411-T-C | Likely benign (Nov 21, 2021) | |||
21-14163413-A-T | Benign (Jun 29, 2023) | |||
21-14163448-A-G | not specified | Uncertain significance (Sep 13, 2023) | ||
21-14163469-G-A | not specified | Uncertain significance (Feb 05, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LIPI | protein_coding | protein_coding | ENST00000344577 | 10 | 102033 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.02e-19 | 0.000321 | 125692 | 0 | 47 | 125739 | 0.000187 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.365 | 261 | 245 | 1.07 | 0.0000112 | 3179 |
Missense in Polyphen | 100 | 92.14 | 1.0853 | 1184 | ||
Synonymous | -0.516 | 93 | 86.9 | 1.07 | 0.00000413 | 862 |
Loss of Function | -1.06 | 26 | 20.8 | 1.25 | 8.66e-7 | 297 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000548 | 0.000543 |
Ashkenazi Jewish | 0.0000994 | 0.0000992 |
East Asian | 0.000381 | 0.000381 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.000160 | 0.000158 |
Middle Eastern | 0.000381 | 0.000381 |
South Asian | 0.000197 | 0.000196 |
Other | 0.000500 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes specifically phosphatidic acid (PA) to produce 2-acyl lysophosphatidic acid (LPA; a potent bioactive lipid mediator) and fatty acid. Does not hydrolyze other phospholipids, like phosphatidylserine (PS), phosphatidylcholine (PC) and phosphatidylethanolamine (PE) or triacylglycerol (TG). {ECO:0000269|PubMed:12963729}.;
- Pathway
- Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA
(Consensus)
Intolerance Scores
- loftool
- 0.241
- rvis_EVS
- 1.2
- rvis_percentile_EVS
- 92.95
Haploinsufficiency Scores
- pHI
- 0.192
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.124
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Lipi
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- phosphatidic acid biosynthetic process;lipid catabolic process
- Cellular component
- extracellular region;plasma membrane
- Molecular function
- phospholipase activity;heparin binding;carboxylic ester hydrolase activity