DACH2
Basic information
Region (hg38): X:86148451-86832604
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 31 | 31 | ||||
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 | 31 | 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-86148628-T-C | not specified | Uncertain significance (Apr 12, 2024) | ||
X-86148634-C-T | not specified | Uncertain significance (Oct 27, 2021) | ||
X-86148709-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
X-86148753-A-G | not specified | Uncertain significance (Sep 05, 2024) | ||
X-86148774-A-G | not specified | Uncertain significance (Jan 18, 2023) | ||
X-86148792-G-A | not specified | Uncertain significance (Mar 31, 2024) | ||
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-86514289-G-A | not specified | Uncertain significance (Nov 07, 2024) | ||
X-86514295-C-G | not specified | Uncertain significance (Oct 25, 2024) | ||
X-86514335-G-A | not specified | Uncertain significance (May 21, 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-86651057-C-A | not specified | Uncertain significance (Oct 20, 2024) | ||
X-86651063-C-T | not specified | Uncertain significance (Sep 25, 2024) | ||
X-86651098-A-G | not specified | Uncertain significance (Nov 09, 2024) | ||
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-86695149-C-G | not specified | Uncertain significance (Sep 30, 2024) | ||
X-86695178-T-C | Likely benign (Jan 01, 2023) | |||
X-86714561-A-G | Likely benign (Mar 01, 2023) |
GnomAD
Source:
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:
- 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