CDS2
CDP-diacylglycerol synthase 2
Basic information
Region (hg38): 20:5126879-5197887
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 CDS2 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 CDS2
This is a list of pathogenic ClinVar variants found in the CDS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-5173587-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
| 20-5173620-C-T | not specified | Uncertain significance (May 03, 2023) | ||
| 20-5176657-G-A | not specified | Uncertain significance (Sep 26, 2022) | ||
| 20-5176702-G-A | not specified | Uncertain significance (May 17, 2023) | ||
| 20-5178845-T-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 20-5178926-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
| 20-5185789-T-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 20-5185806-A-G | not specified | Uncertain significance (Jul 09, 2021) | ||
| 20-5186790-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 20-5186802-A-G | not specified | Uncertain significance (Jul 05, 2023) | ||
| 20-5189103-A-G | not specified | Uncertain significance (Oct 18, 2021) | ||
| 20-5189825-G-A | not specified | Uncertain significance (Dec 28, 2022) | ||
| 20-5190173-A-G | not specified | Uncertain significance (Jun 05, 2023) | ||
| 20-5190176-C-T | not specified | Uncertain significance (Oct 13, 2023) | ||
| 20-5190182-G-A | not specified | Uncertain significance (Sep 21, 2023) | ||
| 20-5190215-C-G | not specified | Uncertain significance (Apr 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDS2 | protein_coding | protein_coding | ENST00000460006 | 13 | 71102 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.86e-7 | 0.975 | 125705 | 0 | 43 | 125748 | 0.000171 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.40 | 147 | 255 | 0.577 | 0.0000140 | 2941 |
| Missense in Polyphen | 31 | 91.049 | 0.34047 | 1118 | ||
| Synonymous | 0.325 | 93 | 97.1 | 0.958 | 0.00000563 | 843 |
| Loss of Function | 2.10 | 14 | 25.4 | 0.551 | 0.00000125 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000580 | 0.0000580 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.000739 | 0.000739 |
| European (Non-Finnish) | 0.000167 | 0.000167 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Provides CDP-diacylglycerol, an important precursor for the synthesis of phosphatidylinositol, phosphatidylglycerol, and cardiolipin.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG
(Consensus)
Recessive Scores
- pRec
- 0.0815
Intolerance Scores
- loftool
- 0.697
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.69
Haploinsufficiency Scores
- pHI
- 0.0816
- hipred
- N
- hipred_score
- 0.362
- ghis
- 0.545
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.558
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cds2
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic system phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- phosphatidylglycerol biosynthetic process;CDP-diacylglycerol biosynthetic process
- Cellular component
- mitochondrial inner membrane;endoplasmic reticulum membrane;membrane;integral component of membrane
- Molecular function
- phosphatidate cytidylyltransferase activity