DACH2

dachshund family transcription factor 2

Basic information

Region (hg38): X:86148451-86832604

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.

not_specified (60 variants)
not_provided (5 variants)
Abnormality_of_neuronal_migration (1 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. These statistics are base on transcript: NM_000053281.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			58 clinvar	1 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	5	1

Loading clinvar variants...

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