DACT3

dishevelled binding antagonist of beta catenin 3, the group of dishevelled binding antagonist of beta catenin family

Basic information

Region (hg38): 19:46647551-46661182

Previous symbols: [ "RRR1" ]

Links

ENSG00000197380 ∙ NCBI:147906 ∙ OMIM:611112 ∙ HGNC:30745 ∙ Uniprot:Q96B18 ∙ 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 DACT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DACT3 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						0
missense			45			45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	46	0	0

Variants in DACT3

This is a list of pathogenic ClinVar variants found in the DACT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46648490-T-C		not specified	Uncertain significance (Jan 26, 2023)
19-46648511-C-A		not specified	Uncertain significance (Aug 30, 2022)
19-46648565-C-A		not specified	Uncertain significance (Nov 18, 2022)
19-46648565-C-G		not specified	Uncertain significance (Dec 16, 2023)
19-46648574-T-C		not specified	Uncertain significance (Oct 16, 2024)
19-46648745-C-T		not specified	Uncertain significance (Oct 17, 2024)
19-46648805-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-46648837-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-46648894-C-G		not specified	Uncertain significance (Aug 30, 2022)
19-46648916-C-T		not specified	Uncertain significance (Oct 25, 2024)
19-46648933-G-A		not specified	Uncertain significance (May 03, 2023)
19-46648943-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-46648997-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-46649047-G-A		not specified	Uncertain significance (Sep 08, 2024)
19-46649066-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-46649113-T-C		not specified	Uncertain significance (Jul 30, 2023)
19-46649114-T-C		not specified	Uncertain significance (Dec 12, 2022)
19-46649131-C-G		not specified	Uncertain significance (Jun 23, 2023)
19-46649138-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-46649200-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-46649261-G-A		not specified	Uncertain significance (Jan 31, 2022)
19-46649276-C-G		not specified	Uncertain significance (Jun 18, 2021)
19-46649284-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-46649300-G-C		not specified	Uncertain significance (Aug 08, 2022)
19-46649354-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DACT3	protein_coding	protein_coding	ENST00000391916	4	13527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.506	0.491	115441	0	2	115443	0.00000866

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	116	195	0.594	0.0000120	3792
Missense in Polyphen		60	89.457	0.67071		1442
Synonymous	1.95	68	91.7	0.741	0.00000618	1515
Loss of Function	2.42	2	10.4	0.191	4.60e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000589	0.0000589
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: May be involved in regulation of intracellular signaling pathways during development. Specifically thought to play a role in canonical and/or non-canonical Wnt signaling pathways through interaction with DSH (Dishevelled) family proteins. {ECO:0000269|PubMed:18538736}.

Haploinsufficiency Scores

• pHI: 0.390
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dact3
• Phenotype: skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of epithelial to mesenchymal transition;Wnt signaling pathway;regulation of Wnt signaling pathway;negative regulation of Wnt signaling pathway;negative regulation of cell growth;negative regulation of canonical Wnt signaling pathway
• Cellular component: cytoplasm
• Molecular function: protein kinase C binding;beta-catenin binding;identical protein binding;protein kinase A binding;delta-catenin binding