CAND2

protein-coding

cullin associated and neddylation dissociated 2 (putative), the group of Armadillo like helical domain containing

Gene summary

Predicted to enable TBP-class protein binding activity. Predicted to be involved in SCF complex assembly; positive regulation of DNA-templated transcription; and protein ubiquitination. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001162499.2

Inheritance

—

ClinVar variants

U:237B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr3:12,796,472-12,834,804

External References & Databases

Ensembl (ENSG00000144712)

Transcript & Mutation Effects

hg38 • Region Span ~38.3 kb

Loading mutation effect viewer...

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 CAND2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 235

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001162499.2. 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			4 clinvar	8 clinvar	1 clinvar	13
missense			232 clinvar	6 clinvar	4 clinvar	242
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	237	14	5	256

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001162499.2	RefSeq	NP_001155971.1	15	MANE Select
ENST00000456430.6	Ensembl	ENSP00000387641.2	15	MANE Select
NM_012298.3	RefSeq	NP_036430.1	13	Standard
ENST00000295989.10	Ensembl	ENSP00000295989.5	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

SCF complex assembly
protein ubiquitination
positive regulation of transcription, DNA-templated

Molecular Function

protein binding
TBP-class protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000456430
Coding exons: 15
Length: 75445
Individuals with no LoFs: 125098
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 125180
p: 0.000328

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.34	646	749	0.862	0.0000474	7853
Missense (PolyPhen)		219	251.91	0.86936		2728
Synonymous	-0.803	356	337	1.06	0.0000218	2717
Loss of Function	1.88	31	44.6	0.696	0.00000245	477

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00096	0.00088	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000095	0.000093	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00040	0.00039	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable assembly factor of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complexes that promotes the exchange of the substrate-recognition F-box subunit in SCF complexes, thereby playing a key role in the cellular repertoire of SCF complexes. {ECO:0000250}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.765
RVIS EVS: 1.53
RVIS percentile EVS: 95.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.831

Gene Damage Prediction

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