CCDC9B

protein-coding

coiled-coil domain containing 9B

Gene summary

Enables RNA binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C15orf52

MANE transcript

NM_207380.3

Inheritance

—

ClinVar variants

U:6B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr15:40,331,452-40,340,939

External References & Databases

Ensembl (ENSG00000188549)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 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 CCDC9B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 5

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207380.3. 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			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	1	0	7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207380.3	RefSeq	NP_997263.3	11	MANE Select
ENST00000397536.7	Ensembl	ENSP00000380670.3	11	MANE Select
ENST00000560922.1	Ensembl	ENSP00000453500.1	5	Standard
ENST00000906859.1	Ensembl	ENSP00000576918.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000559313
Coding exons: 11
Length: 9516
Individuals with no LoFs: 125621
Homozygous LoFs: 1
Heterozygous LoFs: 119
Defined: 125741
p: 0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.577	344	315	1.09	0.0000190	3361
Missense (PolyPhen)		121	102.62	1.1791		1109
Synonymous	-0.303	127	123	1.03	0.00000748	1107
Loss of Function	0.960	23	28.5	0.806	0.00000146	298

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00031	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.0026	0.0026	notable
Other	0.00083	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0819

Intolerance Scores

RVIS EVS: -0.24
RVIS percentile EVS: 36.23

Essentials

Essential (gene trap): N