CAND2

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

Basic information

Region (hg38): 3:12796472-12834804

Links

ENSG00000144712 ∙ NCBI:23066 ∙ OMIM:610403 ∙ HGNC:30689 ∙ Uniprot:O75155 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAND2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAND2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	1	6
missense			120	5	4	129
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	120	10	5

Variants in CAND2

This is a list of pathogenic ClinVar variants found in the CAND2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-12803514-C-T			Likely benign (Nov 01, 2024)
3-12803545-C-A		not specified	Uncertain significance (Dec 21, 2022)
3-12803603-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-12803628-A-G		not specified	Uncertain significance (Jun 10, 2024)
3-12807306-C-T		not specified	Likely benign (Apr 06, 2024)
3-12807314-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-12807362-C-T		not specified	Uncertain significance (Sep 21, 2023)
3-12807379-C-T		not specified	Uncertain significance (Jun 18, 2024)
3-12807380-G-A		not specified	Uncertain significance (Dec 25, 2024)
3-12807398-T-C		not specified	Uncertain significance (Mar 28, 2024)
3-12807412-G-A		not specified	Uncertain significance (May 17, 2023)
3-12807426-G-C		not specified	Uncertain significance (May 30, 2024)
3-12807448-C-G		not specified	Uncertain significance (Aug 02, 2021)
3-12807457-A-G		not specified	Uncertain significance (Dec 10, 2024)
3-12810078-G-A		not specified	Uncertain significance (Sep 25, 2024)
3-12810151-C-T		not specified	Uncertain significance (Nov 15, 2024)
3-12810176-G-A		not specified	Likely benign (Aug 26, 2024)
3-12810210-G-A			Likely benign (Oct 01, 2022)
3-12810298-T-G		not specified	Uncertain significance (Dec 07, 2021)
3-12810321-C-G		not specified	Uncertain significance (Dec 17, 2023)
3-12812995-C-T		not specified	Uncertain significance (Jul 22, 2024)
3-12813313-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-12813335-G-A		not specified	Uncertain significance (Mar 06, 2023)
3-12813374-A-T			Likely benign (May 01, 2023)
3-12815165-A-G		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAND2	protein_coding	protein_coding	ENST00000456430	15	75445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.33e-16	0.708	125098	0	82	125180	0.000328

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	646	749	0.862	0.0000474	7853
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00111
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.000111	0.000111
Finnish	0.0000953	0.0000928
European (Non-Finnish)	0.000360	0.000352
Middle Eastern	0.000111	0.000111
South Asian	0.000400	0.000392
Other	0.000498	0.000492

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.423
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.831

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cand2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: SCF complex assembly;protein ubiquitination;positive regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: protein binding;TBP-class protein binding