CCDC69

coiled-coil domain containing 69

Basic information

Region (hg38): 5:151181051-151224093

Links

ENSG00000198624 ∙ NCBI:26112 ∙ OMIM:619288 ∙ HGNC:24487 ∙ Uniprot:A6NI79 ∙ 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 CCDC69 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC69 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in CCDC69

This is a list of pathogenic ClinVar variants found in the CCDC69 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151183446-G-A			Likely benign (Nov 01, 2022)
5-151183522-A-G		not specified	Uncertain significance (Feb 22, 2023)
5-151183532-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-151183570-T-C		not specified	Uncertain significance (Dec 13, 2022)
5-151183573-T-G		not specified	Uncertain significance (Aug 02, 2022)
5-151183592-G-C		not specified	Uncertain significance (Jan 27, 2022)
5-151183613-G-T		not specified	Uncertain significance (Dec 28, 2022)
5-151184404-G-T		not specified	Uncertain significance (Jan 04, 2024)
5-151185466-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-151185521-C-G		not specified	Uncertain significance (Jul 13, 2021)
5-151186040-A-C		not specified	Uncertain significance (Mar 04, 2024)
5-151186047-G-T		not specified	Uncertain significance (Nov 30, 2022)
5-151187394-T-C		not specified	Likely benign (Sep 07, 2022)
5-151187427-C-T		not specified	Uncertain significance (Feb 01, 2023)
5-151187453-C-T		not specified	Likely benign (Dec 26, 2023)
5-151199015-T-A		not specified	Uncertain significance (Sep 14, 2022)
5-151199020-C-T		not specified	Uncertain significance (Nov 21, 2023)
5-151201586-T-C		not specified	Uncertain significance (Dec 15, 2023)
5-151201589-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-151201619-T-C		not specified	Uncertain significance (Dec 07, 2023)
5-151201650-G-A		not specified	Uncertain significance (Aug 21, 2023)
5-151205471-C-T		not specified	Likely benign (Jul 20, 2021)
5-151223935-T-G		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC69	protein_coding	protein_coding	ENST00000355417	9	43094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.91e-12	0.105	125608	0	140	125748	0.000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.327	178	166	1.07	0.00000937	1914
Missense in Polyphen		53	42.268	1.2539		569
Synonymous	-0.598	70	63.9	1.10	0.00000323	549
Loss of Function	0.542	19	21.7	0.875	0.00000125	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00188	0.00183
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000383	0.000326
Finnish	0.000841	0.000832
European (Non-Finnish)	0.000491	0.000484
Middle Eastern	0.000383	0.000326
South Asian	0.000672	0.000653
Other	0.000995	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a scaffold to regulate the recruitment and assembly of spindle midzone components. Required for the localization of AURKB and PLK1 to the spindle midzone. {ECO:0000305|PubMed:20962590}.

Intolerance Scores

• loftool: 0.894
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.54

Haploinsufficiency Scores

• pHI: 0.0780
• hipred: N
• hipred_score: 0.146
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc69

Gene ontology

• Biological process: spindle midzone assembly
• Cellular component: nucleus;cytoplasm;microtubule cytoskeleton;midbody;spindle midzone
• Molecular function: microtubule binding