LCLAT1
lysocardiolipin acyltransferase 1, the group of 1-acylglycerol-3-phosphate O-acyltransferases
Basic information
Region (hg38): 2:30447226-30644225
Previous symbols: [ "LYCAT" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCLAT1 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 | 16 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 2 | 0 |
Variants in LCLAT1
This is a list of pathogenic ClinVar variants found in the LCLAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-30459661-A-G | not specified | Likely benign (Jun 07, 2023) | ||
| 2-30459668-A-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 2-30459689-C-T | not specified | Likely benign (Mar 28, 2024) | ||
| 2-30525606-G-A | not specified | Uncertain significance (Aug 23, 2021) | ||
| 2-30525654-A-G | not specified | Uncertain significance (Oct 26, 2021) | ||
| 2-30525696-C-T | not specified | Uncertain significance (Jun 12, 2023) | ||
| 2-30525723-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
| 2-30533116-G-A | not specified | Uncertain significance (May 24, 2024) | ||
| 2-30533194-A-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 2-30533299-G-A | not specified | Likely benign (Jun 28, 2023) | ||
| 2-30562182-A-G | not specified | Uncertain significance (Sep 22, 2023) | ||
| 2-30562220-A-G | not specified | Uncertain significance (Oct 02, 2023) | ||
| 2-30568102-G-A | not specified | Uncertain significance (Apr 22, 2024) | ||
| 2-30568158-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 2-30640257-A-G | not specified | Uncertain significance (Aug 22, 2023) | ||
| 2-30640315-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 2-30640343-G-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 2-30640359-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 2-30640367-T-G | not specified | Uncertain significance (Mar 27, 2023) | ||
| 2-30640398-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 2-30640534-T-C | not specified | Uncertain significance (Jun 07, 2023) | ||
| 2-30640538-T-G | not specified | Uncertain significance (Jun 16, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LCLAT1 | protein_coding | protein_coding | ENST00000309052 | 6 | 197000 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000255 | 0.985 | 125721 | 0 | 27 | 125748 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.923 | 189 | 228 | 0.828 | 0.0000118 | 2753 |
| Missense in Polyphen | 30 | 59.562 | 0.50367 | 716 | ||
| Synonymous | -1.04 | 89 | 77.3 | 1.15 | 0.00000396 | 749 |
| Loss of Function | 2.15 | 9 | 19.2 | 0.470 | 9.59e-7 | 218 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000186 | 0.000185 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000102 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Acyl-CoA:lysocardiolipin acyltransferase. Possesses both lysophosphatidylinositol acyltransferase (LPIAT) and lysophosphatidylglycerol acyltransferase (LPGAT) activities. Recognizes both monolysocardiolipin and dilysocardiolipin as substrates with a preference for linoleoyl-CoA and oleoyl-CoA as acyl donors. Acts as a remodeling enzyme for cardiolipin, a major membrane polyglycerophospholipid. Converts lysophosphatidic acid (LPA) into phosphatidic acid (PA) with a relatively low activity. Required for establishment of the hematopoietic and endothelial lineages. {ECO:0000269|PubMed:16620771, ECO:0000269|PubMed:19075029}.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Acyl chain remodeling of CL;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.317
- rvis_EVS
- -0.11
- rvis_percentile_EVS
- 45.26
Haploinsufficiency Scores
- pHI
- 0.295
- hipred
- N
- hipred_score
- 0.254
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.530
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lclat1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- lclat1
- Affected structure
- endothelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- phospholipid metabolic process;phosphatidic acid biosynthetic process;multicellular organism development;CDP-diacylglycerol biosynthetic process;cardiolipin acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;membrane;integral component of membrane
- Molecular function
- 1-acylglycerol-3-phosphate O-acyltransferase activity;protein binding;O-acyltransferase activity;transferase activity, transferring acyl groups