CDS1

CDP-diacylglycerol synthase 1

Basic information

Region (hg38): 4:84583127-84651334

Links

ENSG00000163624 ∙ NCBI:1040 ∙ OMIM:603548 ∙ HGNC:1800 ∙ Uniprot:Q92903 ∙ 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 CDS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDS1 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					1	1
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				3		3
non coding				1	1	2
Total	0	0	14	4	3

Variants in CDS1

This is a list of pathogenic ClinVar variants found in the CDS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-84583394-A-G		CDS1-related disorder	Likely benign (May 20, 2019)
4-84583420-C-T		not specified	Uncertain significance (May 06, 2024)
4-84583421-G-A		not specified	Uncertain significance (Mar 04, 2024)
4-84583454-C-G		not specified	Uncertain significance (Jan 08, 2024)
4-84583457-C-T		not specified	Uncertain significance (May 18, 2023)
4-84604268-G-C		CDS1-related disorder	Likely benign (Mar 16, 2020)
4-84604289-A-G		not specified	Uncertain significance (Apr 05, 2023)
4-84604313-C-T		not specified	Uncertain significance (Jun 11, 2021)
4-84609493-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-84617573-A-G		not specified	Uncertain significance (Jan 16, 2024)
4-84617591-C-A		not specified	Uncertain significance (Dec 26, 2023)
4-84617640-C-T		not specified	Uncertain significance (Feb 23, 2023)
4-84633921-T-C		not specified	Uncertain significance (Oct 29, 2021)
4-84635255-T-A		CDS1-related disorder	Benign (Aug 14, 2019)
4-84635255-T-TA		CDS1-related disorder	Likely benign (Jan 14, 2020)
4-84635256-A-T			Likely benign (Jul 31, 2018)
4-84638915-C-CTTT		CDS1-related disorder	Likely benign (Jan 29, 2020)
4-84640909-C-T		CDS1-related disorder	Benign (Apr 24, 2019)
4-84640964-C-G		not specified	Uncertain significance (Aug 12, 2022)
4-84643057-A-G		CDS1-related disorder • not specified	Uncertain significance (Sep 01, 2021)
4-84645259-T-C		not specified	Uncertain significance (Mar 29, 2023)
4-84645288-G-T		CDS1-related disorder	Uncertain significance (Aug 25, 2023)
4-84648549-A-G		CDS1-related disorder	Likely benign (Jul 12, 2019)
4-84648571-G-A		CDS1-related disorder	Benign (Oct 28, 2019)
4-84648584-G-T		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDS1	protein_coding	protein_coding	ENST00000295887	13	68360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000641	0.999	125712	0	29	125741	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	170	234	0.727	0.0000109	3005
Missense in Polyphen		50	84.492	0.59177		1143
Synonymous	2.06	59	82.8	0.713	0.00000385	863
Loss of Function	2.91	10	26.0	0.385	0.00000118	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000392
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000987	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Provides CDP-diacylglycerol, an important precursor for the synthesis of phosphatidylinositol (PtdIns), phosphatidylglycerol, and cardiolipin. Overexpression may amplify cellular signaling responses from cytokines. May also play an important role in the signal transduction mechanism of retina and neural cells.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Synthesis of PI;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0926

Intolerance Scores

• loftool: 0.614
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.544
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cds1

Zebrafish Information Network

• Gene name: cds1
• Affected structure: intersegmental vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: CDP-choline pathway;phosphatidylinositol biosynthetic process;signal transduction;phototransduction;CDP-diacylglycerol biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: diacylglycerol cholinephosphotransferase activity;phosphatidate cytidylyltransferase activity