CC2D2B

protein-coding

coiled-coil and C2 domain containing 2B

Gene summary

Predicted to be involved in non-motile cilium assembly and protein localization to ciliary transition zone. Predicted to be active in ciliary transition zone. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf130
C10orf131

MANE transcript

NM_001349008.3

Inheritance

—

ClinVar variants

U:52B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr10:95,907,603-96,033,745

External References & Databases

Ensembl (ENSG00000188649)

Transcript & Mutation Effects

hg38 • Region Span ~126.1 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 CC2D2B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001349008.3. 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	3 clinvar		4
missense			48 clinvar	1 clinvar		49
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	52	4	0	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001349008.3	RefSeq	NP_001335937.1	34	MANE Select
ENST00000646931.3	Ensembl	ENSP00000496666.2	34	MANE Select
NM_001001732.4	RefSeq	NP_001001732.2	8	Standard
NM_001130446.3	RefSeq	NP_001123918.2	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000410012
Coding exons: 10
Length: 58656
Individuals with no LoFs: 124652
Homozygous LoFs: 0
Heterozygous LoFs: 124
Defined: 124776
p: 0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	147	198	0.743	0.00000924	2667
Missense (PolyPhen)		49	63.144	0.776		862
Synonymous	1.15	56	68.1	0.823	0.00000344	704
Loss of Function	1.69	15	23.9	0.627	0.00000130	281

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.0021	0.0020	notable
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.671
RVIS EVS: 0.35
RVIS percentile EVS: 74.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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