DLX6
Basic information
Region (hg38): 7:97005553-97011040
Links
Phenotypes
GenCC
Source:
- split hand-foot malformation (Supportive), mode of inheritance: AD
- autism spectrum disorder (Limited), mode of inheritance: AD
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 DLX6 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 | 18 | 21 | ||||
missense | 17 | 19 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 25 | 31 | ||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 7 | |||||
Total | 0 | 0 | 42 | 26 | 10 |
Variants in DLX6
This is a list of pathogenic ClinVar variants found in the DLX6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-97006014-G-A | not specified | Uncertain significance (Sep 25, 2023) | ||
7-97006028-C-T | Benign (Nov 14, 2023) | |||
7-97006051-GGCA-G | Benign (Mar 24, 2021) | |||
7-97006051-GGCAGCA-G | DLX6-related disorder | Uncertain significance (Apr 10, 2023) | ||
7-97006051-GGCAGCAGCA-G | Uncertain significance (Mar 02, 2023) | |||
7-97006051-G-GGCA | DLX6-related disorder | Uncertain significance (Aug 07, 2023) | ||
7-97006051-G-GGCAGCA | Uncertain significance (Aug 17, 2023) | |||
7-97006051-G-GGCAGCAGCAGCA | DLX6-related disorder | Uncertain significance (Sep 21, 2023) | ||
7-97006051-G-GGCAGCAGCAGCAGCA | Uncertain significance (Jul 15, 2022) | |||
7-97006052-GCAGCAGCAGCAGCAGCAGCAGCAA-G | Uncertain significance (Jun 18, 2022) | |||
7-97006052-G-GCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAA | Uncertain significance (Jul 14, 2023) | |||
7-97006052-G-GCAGCAGCAGCAGCAGCAGCAGCAA | not specified | Conflicting classifications of pathogenicity (Dec 06, 2023) | ||
7-97006055-GCAGCAGCAGCAGCAGCAGCAA-G | Uncertain significance (Sep 05, 2023) | |||
7-97006055-G-GCAGCAGCAGCAGCAGCAGCAA | Uncertain significance (Nov 30, 2022) | |||
7-97006058-GCAGCAGCAGCAGCAGCAA-G | Uncertain significance (Aug 04, 2023) | |||
7-97006061-GCAGCAGCAGCAGCAA-G | Uncertain significance (Aug 17, 2023) | |||
7-97006064-G-GCAGCAGCAGCAA | Uncertain significance (Jun 22, 2023) | |||
7-97006070-G-A | DLX6-related disorder | Likely benign (Dec 08, 2021) | ||
7-97006076-A-G | Likely benign (Apr 10, 2023) | |||
7-97006076-A-ACAG | DLX6-related disorder | Uncertain significance (Apr 09, 2023) | ||
7-97006076-A-ACAGCAGCAG | Uncertain significance (Aug 03, 2023) | |||
7-97006079-G-A | Likely benign (Mar 01, 2023) | |||
7-97006080-C-G | Uncertain significance (Nov 15, 2023) | |||
7-97006081-AGCAGCAGCAGCAGCAGCAACAGCAACA-C | Uncertain significance (Dec 08, 2021) | |||
7-97006082-G-A | Likely benign (Dec 07, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DLX6 | protein_coding | protein_coding | ENST00000518156 | 3 | 5492 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.921 | 0.0786 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.17 | 105 | 145 | 0.726 | 0.00000682 | 1888 |
Missense in Polyphen | 27 | 61.834 | 0.43665 | 747 | ||
Synonymous | -2.27 | 79 | 57.2 | 1.38 | 0.00000276 | 537 |
Loss of Function | 3.02 | 1 | 12.5 | 0.0797 | 5.45e-7 | 135 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
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:
- Pathway
- MECP2 and Associated Rett Syndrome;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Validated transcriptional targets of deltaNp63 isoforms;Regulation of RUNX2 expression and activity
(Consensus)
Recessive Scores
- pRec
- 0.183
Intolerance Scores
- loftool
- 0.257
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.649
- hipred
- Y
- hipred_score
- 0.808
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dlx6
- Phenotype
- craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;
Gene ontology
- Biological process
- skeletal system development;regulation of transcription by RNA polymerase II;nervous system development;cell differentiation;embryonic limb morphogenesis;epithelial cell differentiation;inner ear morphogenesis;positive regulation of transcription by RNA polymerase II;anatomical structure formation involved in morphogenesis;positive regulation of epithelial cell proliferation;roof of mouth development;head development
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding