CDS2

CDP-diacylglycerol synthase 2

Basic information

Region (hg38): 20:5126878-5197887

Links

ENSG00000101290 ∙ NCBI:8760 ∙ OMIM:603549 ∙ HGNC:1801 ∙ Uniprot:O95674 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDS2 gene.

• Inborn genetic diseases (11 variants)

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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	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)
20-5185789-T-C		not specified	Uncertain significance (Nov 10, 2022)
20-5185806-A-G		not specified	Uncertain significance (Jul 09, 2021)
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: gnomAD

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: dbNSFP

• 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