CIDEC

cell death inducing DFFA like effector c

Basic information

Region (hg38): 3:9866711-9880255

Links

ENSG00000187288 ∙ NCBI:63924 ∙ OMIM:612120 ∙ HGNC:24229 ∙ Uniprot:Q96AQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• CIDEC-related familial partial lipodystrophy (Supportive), mode of inheritance: AR
• CIDEC-related familial partial lipodystrophy (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lipodystrophy, familial partial, type 5	AR	Cardiovascular; Endocrine; Gastrointestinal	Medical treatment of factors such as diabetes, hypertension, and lipid abnormalities may be beneficial to reduce morbidity/mortality; Recognition and treatment of hypertriglyceridemia can help avoid sequelae such as acute pancreatitis	Cardiovascular; Endocrine; Gastrointestinal	20049731

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIDEC 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	2	3
missense			20	4	5	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	9	10
Total	0	0	20	6	16

Variants in CIDEC

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

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

Position	Type	Phenotype	Significance	ClinVar
3-9866841-A-G			Benign (Nov 10, 2018)
3-9866972-C-T			Benign (Jun 18, 2021)
3-9867065-G-C			Benign (Jun 18, 2021)
3-9867171-G-A		not specified	Uncertain significance (May 25, 2022)
3-9867175-C-G		not specified	Uncertain significance (Jan 18, 2022)
3-9867191-C-A		CIDEC-related disorder	Likely benign (Oct 27, 2020)
3-9867248-T-C		CIDEC-related disorder	Benign (Apr 02, 2018)
3-9867251-G-A		not specified • CIDEC-related disorder	Benign (Nov 10, 2018)
3-9867257-T-C		not specified	Likely benign (Apr 02, 2018)
3-9867263-C-T			Likely benign (Dec 31, 2019)
3-9867266-C-T		not specified	Uncertain significance (Jan 31, 2022)
3-9867286-G-A		not specified	Uncertain significance (May 13, 2024)
3-9867295-C-A		CIDEC-related familial partial lipodystrophy	Pathogenic (Aug 01, 2009)
3-9869889-T-A		not specified	Uncertain significance (May 24, 2024)
3-9869891-C-T		not specified	Uncertain significance (May 22, 2018)
3-9869969-A-G		not specified	Uncertain significance (Sep 14, 2022)
3-9870012-G-A		not specified	Uncertain significance (Jan 13, 2023)
3-9870047-A-G		not specified	Uncertain significance (May 18, 2022)
3-9870049-G-C			Likely benign (Aug 03, 2017)
3-9870056-G-A		not specified	Uncertain significance (Oct 10, 2023)
3-9870065-G-A		not specified	Uncertain significance (Mar 28, 2024)
3-9870154-G-A		CIDEC-related disorder	Likely benign (Dec 16, 2022)
3-9870174-G-A		not specified	Uncertain significance (Sep 30, 2021)
3-9870190-G-C		not specified	Uncertain significance (Jan 22, 2024)
3-9870201-A-G		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIDEC	protein_coding	protein_coding	ENST00000430427	6	13541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00897	0.942	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.669	163	141	1.16	0.00000855	1591
Missense in Polyphen		45	43.058	1.0451		519
Synonymous	-1.02	68	58.1	1.17	0.00000347	501
Loss of Function	1.71	5	11.2	0.448	5.48e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000665	0.000665
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to lipid droplets and regulates their enlargement, thereby restricting lipolysis and favoring storage. At focal contact sites between lipid droplets, promotes directional net neutral lipid transfer from the smaller to larger lipid droplets. The transfer direction may be driven by the internal pressure difference between the contacting lipid droplet pair. Its role in neutral lipid transfer and lipid droplet enlargement is activated by the interaction with PLIN1. May act as a CEBPB coactivator in the white adipose tissue to control the expression of a subset of CEBPB downstream target genes, including SOCS1, SOCS3, TGFB1, TGFBR1, ID2 and XDH. When overexpressed in preadipocytes, induces apoptosis or increases cell susceptibility to apoptosis induced by serum deprivation or TGFB treatment. As mature adipocytes, that express high CIDEC levels, are quite resistant to apoptotic stimuli, the physiological significance of its role in apoptosis is unclear. May play a role in the modulation of the response to osmotic stress by preventing NFAT5 to translocate into the nucleus and activate its target genes expression. {ECO:0000269|PubMed:12429024, ECO:0000269|PubMed:18334488, ECO:0000269|PubMed:19843876, ECO:0000269|PubMed:20049731, ECO:0000269|PubMed:23399566}.
• Disease: DISEASE: Note=In omental adipose tissue of obese patients matched for BMI, expression levels tend to correlate with insulin sensitivity. Expression is increased 2-3 fold in the group of patients with high insulin sensitivity, compared to the insulin- resistant group. This observation is consistent with the idea that triglyceride storage in adipocytes plays an important role in sequestering triglycerides and fatty acids away from the circulation and peripheral tissues, thus enhancing insulin sensitivity in liver and muscle. This effect is not significant in subcutaneous adipose tissue (PubMed:18509062). In subcutaneous adipose tissue of diabetic patients, tends to negatively correlate with body mass index and total fat mass, independently of insulin sensitivity (PubMed:18334488). {ECO:0000269|PubMed:18334488, ECO:0000269|PubMed:18509062}.; DISEASE: Lipodystrophy, familial partial, 5 (FPLD5) [MIM:615238]: A form of lipodystrophy characterized by loss of subcutaneous adipose tissue affecting limb, femorogluteal and subcutaneous abdominal fat, preservation of visceral, neck and axilliary fat, hepatomegaly, hepatic steatosis and insulin-resistant diabetes. {ECO:0000269|PubMed:20049731}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Plasma lipoprotein assembly, remodeling, and clearance;Metabolism of lipids;Metabolism;Lipid particle organization (Consensus)

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.170
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.454

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cidec
• Phenotype: normal phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: apoptotic process;lipid droplet organization;execution phase of apoptosis
• Cellular component: nucleus;endoplasmic reticulum;lipid droplet;cytosol
• Molecular function: molecular_function