CDIPT
CDP-diacylglycerol--inositol 3-phosphatidyltransferase
Basic information
Region (hg38): 16:29858357-29863414
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 CDIPT 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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in CDIPT
This is a list of pathogenic ClinVar variants found in the CDIPT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-29859214-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 16-29859235-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 16-29859256-A-G | not specified | Uncertain significance (Jan 03, 2022) | ||
| 16-29859271-G-A | not specified | Uncertain significance (Jul 14, 2021) | ||
| 16-29859314-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 16-29859502-C-A | not specified | Uncertain significance (May 01, 2022) | ||
| 16-29859520-C-A | not specified | Uncertain significance (Dec 03, 2024) | ||
| 16-29860582-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 16-29860655-C-T | not specified | Uncertain significance (Feb 12, 2025) | ||
| 16-29861209-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 16-29861226-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 16-29861239-G-C | not specified | Uncertain significance (Dec 14, 2021) | ||
| 16-29862622-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
| 16-29862684-T-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 16-29862700-C-A | not specified | Uncertain significance (Mar 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDIPT | protein_coding | protein_coding | ENST00000219789 | 6 | 5380 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.130 | 0.850 | 125704 | 0 | 7 | 125711 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.719 | 105 | 128 | 0.821 | 0.00000736 | 1372 |
| Missense in Polyphen | 30 | 44.37 | 0.67614 | 529 | ||
| Synonymous | 0.728 | 47 | 53.8 | 0.874 | 0.00000325 | 434 |
| Loss of Function | 2.01 | 3 | 9.76 | 0.307 | 4.99e-7 | 109 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000445 | 0.0000440 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the biosynthesis of phosphatidylinositol (PtdIns) as well as PtdIns:inositol exchange reaction. May thus act to reduce an excessive cellular PtdIns content. The exchange activity is due to the reverse reaction of PtdIns synthase and is dependent on CMP, which is tightly bound to the enzyme. {ECO:0000269|PubMed:8110188}.;
- Pathway
- Inositol phosphate metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;Phospholipid Biosynthesis;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Metabolism of lipids;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Synthesis of PI;Phosphatidylinositol phosphate metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.362
Intolerance Scores
- loftool
- 0.550
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.142
- hipred
- N
- hipred_score
- 0.285
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.933
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdipt
- 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- cdipt
- Affected structure
- intestinal epithelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;CDP-diacylglycerol metabolic process
- Cellular component
- Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;membrane;integral component of membrane
- Molecular function
- CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity;protein binding;diacylglycerol binding;manganese ion binding;carbohydrate binding;alcohol binding