CCDC3

coiled-coil domain containing 3

Basic information

Region (hg38): 10:12896624-13099652

Links

ENSG00000151468 ∙ NCBI:83643 ∙ ∙ HGNC:23813 ∙ Uniprot:Q9BQI4 ∙ 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 CCDC3 gene.

• Inborn genetic diseases (18 variants)
• Lip and oral cavity carcinoma (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC3 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			17	1		18
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in CCDC3

This is a list of pathogenic ClinVar variants found in the CCDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-12898429-T-G		not specified	Uncertain significance (Jan 19, 2022)
10-12898429-TA-T			Benign (Dec 31, 2019)
10-12898432-G-C		not specified	Uncertain significance (May 23, 2023)
10-12898457-T-G		not specified	Uncertain significance (Jan 24, 2023)
10-12898458-G-C		not specified	Uncertain significance (Aug 08, 2023)
10-12898480-G-A		not specified	Uncertain significance (Dec 13, 2023)
10-12898522-C-A		not specified	Uncertain significance (Dec 20, 2021)
10-12898544-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-12898561-T-A		not specified	Uncertain significance (Jan 26, 2022)
10-12898562-T-C		not specified	Uncertain significance (Jan 26, 2022)
10-12898592-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-12899157-T-C		Lip and oral cavity carcinoma	association not found (Nov 02, 2015)
10-12998371-G-T		not specified	Uncertain significance (Jan 27, 2022)
10-12998378-G-A		not specified	Likely benign (Jun 17, 2022)
10-13001222-C-T		not specified	Uncertain significance (Dec 09, 2023)
10-13001230-A-C		not specified	Uncertain significance (Jun 29, 2023)
10-13001264-C-A		not specified	Uncertain significance (Aug 13, 2021)
10-13001405-G-A		not specified	Uncertain significance (Jan 09, 2024)
10-13001413-G-A		not specified	Uncertain significance (Apr 20, 2023)
10-13001473-T-G		not specified	Uncertain significance (Sep 30, 2022)
10-13001485-C-T		not specified	Uncertain significance (Jun 22, 2021)
10-13001515-G-A		not specified	Uncertain significance (Nov 06, 2023)
10-13001528-G-C		not specified	Uncertain significance (Jun 03, 2022)
10-13001528-G-T		not specified	Uncertain significance (Sep 29, 2022)
10-13001530-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC3	protein_coding	protein_coding	ENST00000378825	3	203026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00487	0.893	125654	0	94	125748	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.849	175	146	1.20	0.00000905	1718
Missense in Polyphen		62	51.047	1.2146		600
Synonymous	-0.0494	66	65.5	1.01	0.00000400	538
Loss of Function	1.39	5	9.66	0.517	4.98e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00187
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00163	0.00163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates TNF-alpha-induced pro-inflammatory response in endothelial cells (ECs) via inhibition of TNF-alpha- induced NF-kappaB activation in ECs (PubMed:25193116). Positively regulates lipid accumulation in adipose cells (By similarity). {ECO:0000250|UniProtKB:Q9D6Y1, ECO:0000269|PubMed:25193116}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.313
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.282
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc3
• Phenotype: homeostasis/metabolism phenotype; 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: negative regulation of tumor necrosis factor-mediated signaling pathway;positive regulation of fat cell differentiation;positive regulation of lipid biosynthetic process
• Cellular component: extracellular region;endoplasmic reticulum