DACH2

dachshund family transcription factor 2

Basic information

Region (hg38): X:86148451-86832604

Links

ENSG00000126733NCBI:117154OMIM:300608HGNC:16814Uniprot:Q96NX9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
DACH2protein_codingprotein_codingENST00000373125 12684146
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1620.835125734271257430.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4711912100.9090.00001513903
Missense in Polyphen5467.8380.796011289
Synonymous0.2667679.00.9620.000005611194
Loss of Function2.60414.80.2700.00000100305

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001160.0000980
Ashkenazi Jewish0.0001370.0000992
East Asian0.00007610.0000544
Finnish0.000.00
European (Non-Finnish)0.00004260.0000264
Middle Eastern0.00007610.0000544
South Asian0.0001430.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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