DACH2

dachshund family transcription factor 2

Basic information

Region (hg38): X:86148450-86832604

Links

ENSG00000126733 ∙ NCBI:117154 ∙ OMIM:300608 ∙ HGNC:16814 ∙ Uniprot:Q96NX9 ∙ 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 DACH2 gene.

• Inborn genetic diseases (19 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DACH2 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		2
missense			19	1		20
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	19	3	0

Variants in DACH2

This is a list of pathogenic ClinVar variants found in the DACH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-86148634-C-T		not specified	Uncertain significance (Oct 27, 2021)
X-86148774-A-G		not specified	Uncertain significance (Jan 18, 2023)
X-86148805-A-G		not specified	Uncertain significance (Apr 12, 2023)
X-86148833-C-T			Likely benign (Mar 01, 2023)
X-86148993-G-A		not specified	Uncertain significance (Feb 05, 2024)
X-86149017-G-A		not specified	Uncertain significance (Apr 27, 2023)
X-86149074-T-C		not specified	Uncertain significance (Jan 29, 2024)
X-86514374-G-A		not specified	Uncertain significance (Jun 02, 2023)
X-86651051-C-T		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-86695040-G-C		not specified	Uncertain significance (May 11, 2022)
X-86695102-C-A		not specified	Uncertain significance (Sep 27, 2022)
X-86695135-C-T		not specified	Uncertain significance (Jul 13, 2021)
X-86695178-T-C			Likely benign (Jan 01, 2023)
X-86714561-A-G			Likely benign (Mar 01, 2023)
X-86714639-C-A		not specified	Uncertain significance (Dec 13, 2022)
X-86714641-A-G		not specified	Uncertain significance (Feb 22, 2023)
X-86714701-C-G		not specified	Uncertain significance (Dec 06, 2022)
X-86714707-C-T		not specified	Uncertain significance (Feb 10, 2022)
X-86739832-G-A		not specified	Uncertain significance (Oct 20, 2023)
X-86812876-C-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-86812915-C-T		not specified	Uncertain significance (Nov 21, 2023)
X-86812916-C-A		not specified	Uncertain significance (Nov 21, 2023)
X-86812932-C-T		not specified	Likely benign (Jan 24, 2024)
X-86812933-G-A		not specified	Uncertain significance (Apr 14, 2023)
X-86812948-C-T		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DACH2	protein_coding	protein_coding	ENST00000373125	12	684146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.162	0.835	125734	2	7	125743	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.471	191	210	0.909	0.0000151	3903
Missense in Polyphen		54	67.838	0.79601		1289
Synonymous	0.266	76	79.0	0.962	0.00000561	1194
Loss of Function	2.60	4	14.8	0.270	0.00000100	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.0000980
Ashkenazi Jewish	0.000137	0.0000992
East Asian	0.0000761	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000426	0.0000264
Middle Eastern	0.0000761	0.0000544
South Asian	0.000143	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that is involved in regulation of organogenesis. Seems to be a regulator for SIX1 and SIX6. Seems to act as a corepressor of SIX6 in regulating proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. Is recruited with SIX6 to the p27Kip1 promoter in embryonal retina. SIX6 corepression seems also to involve NCOR1, TBL1, HDAC1 and HDAC3. May be involved together with PAX3, SIX1, and EYA2 in regulation of myogenesis. In the developing somite, expression of DACH2 and PAX3 is regulated by the overlying ectoderm, and DACH2 and PAX3 positively regulate each other's expression (By similarity). Probably binds to DNA via its DACHbox-N domain. {ECO:0000250}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.0108
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.737
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.329

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dach2
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;development of primary female sexual characteristics
• Cellular component: nucleus;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding