CCDC86

protein-coding

coiled-coil domain containing 86

Gene summary

Enables RNA binding activity. Involved in chromosome segregation and mitotic nuclear division. Located in chromosome; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024098.4

Inheritance

—

ClinVar variants

U:65B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr11:60,842,113-60,851,081

External References & Databases

Ensembl (ENSG00000110104)

Transcript & Mutation Effects

hg38 • Region Span ~9.0 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 CCDC86 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 67

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024098.4. 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 clinvar		2
missense			64 clinvar	2 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	3	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024098.4	RefSeq	NP_077003.1	4	MANE Select
ENST00000227520.10	Ensembl	ENSP00000227520.5	4	MANE Select
ENST00000535217.1	Ensembl	ENSP00000442111.1	2	Standard
ENST00000545580.1	Ensembl	ENSP00000440906.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

viral process

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000227520
Coding exons: 4
Length: 9011
Individuals with no LoFs: 125652
Homozygous LoFs: 0
Heterozygous LoFs: 95
Defined: 125747
p: 0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.485	199	219	0.908	0.0000125	2258
Missense (PolyPhen)		59	67.341	0.87614		666
Synonymous	-0.237	96	93.1	1.03	0.00000460	790
Loss of Function	1.49	10	16.6	0.604	9.00e-7	175

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00047	0.00046	rare
European (Non-Finnish)	0.00072	0.00068	rare
South Asian	0.000065	0.000065	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0941

Intolerance Scores

RVIS EVS: 0.71
RVIS percentile EVS: 85.63

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.919

Gene Damage Prediction

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