CCDC69

protein-coding

coiled-coil domain containing 69

Gene summary

Predicted to enable microtubule binding activity. Involved in spindle midzone assembly. Located in spindle midzone. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015621.3

Inheritance

—

ClinVar variants

U:52B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr5:151,181,052-151,224,093

External References & Databases

Ensembl (ENSG00000198624)

Transcript & Mutation Effects

hg38 • Region Span ~43.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC69 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015621.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			48 clinvar	6 clinvar		54
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	52	7	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015621.3	RefSeq	NP_056436.2	9	MANE Select
ENST00000355417.7	Ensembl	ENSP00000347586.2	9	MANE Select
ENST00000518189.5	Ensembl	ENSP00000430549.1	7	Standard
ENST00000522964.1	Ensembl	ENSP00000428588.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spindle midzone assembly

Molecular Function

microtubule binding

Cellular Component

nucleus
cytoplasm
microtubule cytoskeleton
midbody
spindle midzone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355417
Coding exons: 9
Length: 43094
Individuals with no LoFs: 125608
Homozygous LoFs: 0
Heterozygous LoFs: 140
Defined: 125748
p: 0.000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.327	178	166	1.07	0.00000937	1914
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0016	notable
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00038	0.00033	rare
Finnish	0.00084	0.00083	rare
European (Non-Finnish)	0.00049	0.00048	rare
South Asian	0.00067	0.00065	rare
Other	0.0010	0.00098	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.275

Gene Damage Prediction

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