CCDC93

coiled-coil domain containing 93, the group of CCC complex

Basic information

Region (hg38): 2:117915477-118014133

Links

ENSG00000125633 ∙ NCBI:54520 ∙ ∙ HGNC:25611 ∙ Uniprot:Q567U6 ∙ 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 CCDC93 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC93 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			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in CCDC93

This is a list of pathogenic ClinVar variants found in the CCDC93 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-117920356-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-117920390-G-A		not specified	Uncertain significance (Jun 07, 2023)
2-117931041-T-C		not specified	Uncertain significance (Oct 25, 2022)
2-117935541-C-T		not specified	Uncertain significance (Jul 11, 2023)
2-117935556-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-117935557-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-117939031-C-T		not specified	Uncertain significance (Jun 03, 2022)
2-117939106-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-117941195-G-A		not specified	Uncertain significance (Jul 21, 2022)
2-117941212-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-117941264-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-117944053-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-117944071-G-A		not specified	Uncertain significance (Nov 06, 2023)
2-117949341-C-G		not specified	Uncertain significance (Feb 28, 2024)
2-117952383-G-A		not specified	Uncertain significance (Dec 20, 2022)
2-117958420-C-T		not specified	Uncertain significance (May 31, 2023)
2-117973922-C-T		not specified	Uncertain significance (Jul 14, 2023)
2-117973990-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-117974857-T-C		not specified	Uncertain significance (Dec 14, 2022)
2-117974867-C-T		not specified	Uncertain significance (May 27, 2022)
2-117975249-C-T		not specified	Uncertain significance (Dec 07, 2021)
2-117975255-G-A			Benign (Feb 23, 2021)
2-117975261-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-117986015-G-C		not specified	Uncertain significance (May 17, 2023)
2-117986038-C-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC93	protein_coding	protein_coding	ENST00000376300	24	98656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.79e-8	1.00	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	293	350	0.837	0.0000200	4141
Missense in Polyphen		71	100.09	0.70939		1225
Synonymous	-0.425	126	120	1.05	0.00000659	1118
Loss of Function	3.80	21	50.0	0.420	0.00000284	565

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000925	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000925	0.000925
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association within the CCC complex and cooperation with the WASH complex on early endosomes and is dependent on its interaction with WASHC2C (PubMed:25355947). {ECO:0000269|PubMed:25355947}.

Recessive Scores

• pRec: 0.0860

Intolerance Scores

• loftool: 0.753
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: Y
• hipred_score: 0.554
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc93

Gene ontology

• Biological process: Golgi to plasma membrane transport;protein transport
• Cellular component: early endosome;intracellular membrane-bounded organelle
• Molecular function: protein binding