DACT2

dishevelled binding antagonist of beta catenin 2, the group of dishevelled binding antagonist of beta catenin family

Basic information

Region (hg38): 6:168292830-168319777

Previous symbols: [ "C6orf116" ]

Links

ENSG00000164488 ∙ NCBI:168002 ∙ OMIM:608966 ∙ HGNC:21231 ∙ Uniprot:Q5SW24 ∙ 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 DACT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DACT2 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				2	1	3
missense			79	10		89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	81	12	1

Variants in DACT2

This is a list of pathogenic ClinVar variants found in the DACT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-168307512-G-A		not specified	Uncertain significance (Dec 02, 2024)
6-168307583-G-A		not specified	Uncertain significance (May 21, 2024)
6-168307583-G-T		not specified	Uncertain significance (Dec 12, 2023)
6-168307590-C-T		not specified	Uncertain significance (Jan 09, 2025)
6-168307595-G-A		not specified	Uncertain significance (Mar 07, 2025)
6-168307620-A-G		not specified	Uncertain significance (Jul 28, 2021)
6-168307635-C-T		not specified	Uncertain significance (Sep 26, 2023)
6-168307636-G-A			Benign (Aug 14, 2017)
6-168307647-C-T		not specified	Uncertain significance (May 30, 2023)
6-168307668-G-C		not specified	Uncertain significance (May 31, 2024)
6-168307674-C-T		not specified	Uncertain significance (Dec 11, 2023)
6-168307700-G-T		not specified	Uncertain significance (Nov 09, 2021)
6-168307707-C-T		not specified	Uncertain significance (May 10, 2024)
6-168307710-C-T		not specified	Uncertain significance (May 13, 2022)
6-168307740-G-A		not specified	Uncertain significance (Dec 17, 2024)
6-168307748-C-T		not specified	Uncertain significance (Jan 29, 2025)
6-168307752-C-T		not specified	Uncertain significance (Jan 01, 2025)
6-168307787-G-A		not specified	Uncertain significance (Aug 10, 2021)
6-168307787-G-T		not specified	Uncertain significance (Mar 21, 2023)
6-168307788-T-C		not specified	Likely benign (Mar 06, 2023)
6-168307854-C-T		not specified	Likely benign (Jan 29, 2024)
6-168307860-T-C		not specified	Uncertain significance (Jan 30, 2024)
6-168307899-G-A		not specified	Uncertain significance (Feb 11, 2025)
6-168307938-G-A		not specified	Uncertain significance (Dec 15, 2022)
6-168307972-C-T			Likely benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DACT2	protein_coding	protein_coding	ENST00000366795	4	26925

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00940	0.827	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	340	421	0.808	0.0000266	4855
Missense in Polyphen		95	117.85	0.80613		1567
Synonymous	2.25	156	196	0.796	0.0000138	1713
Loss of Function	1.11	4	7.22	0.554	3.10e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulation of intracellular signaling pathways during development. Negatively regulates the Nodal signaling pathway, possibly by promoting the lysosomal degradation of Nodal receptors, such as TGFBR1. May be involved in control of the morphogenetic behavior of kidney ureteric bud cells by keeping cells epithelial and restraining their mesenchymal character. May play an inhibitory role in the re-epithelialization of skin wounds by attenuating TGF-beta signaling (By similarity). {ECO:0000250}.
• Pathway: Vitamin D Receptor Pathway;TGF-beta receptor signaling (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 1.28
• rvis_percentile_EVS: 93.77

Haploinsufficiency Scores

• pHI: 0.200

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dact2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: dact2
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: epithelial cell morphogenesis;negative regulation of cell adhesion;regulation of Wnt signaling pathway;skin development;inner medullary collecting duct development;negative regulation of nodal signaling pathway
• Cellular component: cytoplasm
• Molecular function: protein kinase C binding;beta-catenin binding;transcription factor binding;protein kinase A binding;delta-catenin binding