CC2D1B

protein-coding

coiled-coil and C2 domain containing 1B, the group of C2 domain containing

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001330585.2

Inheritance

—

ClinVar variants

U:183B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:52,345,723-52,366,205

External References & Databases

Ensembl (ENSG00000154222)

Transcript & Mutation Effects

hg38 • Region Span ~20.5 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 CC2D1B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330585.2. 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			3 clinvar	1 clinvar	3 clinvar	7
missense			169 clinvar	10 clinvar		179
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	183	11	3	197

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330585.2	RefSeq	NP_001317514.1	23	MANE Select
ENST00000284376.8	Ensembl	ENSP00000284376.3	23	MANE Select
NM_032449.3	RefSeq	NP_115825.1	23	Standard
ENST00000371586.6	Ensembl	ENSP00000360642.2	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription repressor activity, RNA polymerase II-specific
protein binding

Cellular Component

nucleus
nucleoplasm
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371586
Coding exons: 23
Length: 20471
Individuals with no LoFs: 125577
Homozygous LoFs: 0
Heterozygous LoFs: 171
Defined: 125748
p: 0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.01	570	506	1.13	0.0000305	5479
Missense (PolyPhen)		187	156.25	1.1968		1725
Synonymous	0.560	193	203	0.950	0.0000121	1768
Loss of Function	2.04	36	51.8	0.694	0.00000304	547

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00096	0.00092	rare
Latino/Admixed American	0.00086	0.00084	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.0013	0.0013	notable
Finnish	0.00043	0.00042	rare
European (Non-Finnish)	0.00054	0.00053	rare
South Asian	0.00090	0.00088	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. {ECO:0000269|PubMed:19423080}.;

Intolerance Scores

LoFtool: 0.877
RVIS EVS: 0.19
RVIS percentile EVS: 66.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.627

Gene Damage Prediction

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