DLX6

distal-less homeobox 6, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 7:97005553-97011040

Links

ENSG00000006377NCBI:1750OMIM:600030HGNC:2919Uniprot:P56179AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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 ClinVar and linked to the DLX6 gene.

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
clinvar
3
clinvar
21
missense
17
clinvar
2
clinvar
19
nonsense
0
start loss
0
frameshift
0
inframe indel
25
clinvar
3
clinvar
3
clinvar
31
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
3
clinvar
4
clinvar
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)3082969
7-97006028-C-T Benign (Nov 14, 2023)1662165
7-97006051-GGCA-G Benign (Mar 24, 2021)1660081
7-97006051-GGCAGCA-G DLX6-related disorder Uncertain significance (Apr 10, 2023)2041393
7-97006051-GGCAGCAGCA-G Uncertain significance (Mar 02, 2023)1373278
7-97006051-G-GGCA DLX6-related disorder Uncertain significance (Aug 07, 2023)1476323
7-97006051-G-GGCAGCA Uncertain significance (Aug 17, 2023)2720424
7-97006051-G-GGCAGCAGCAGCA DLX6-related disorder Uncertain significance (Sep 21, 2023)2915783
7-97006051-G-GGCAGCAGCAGCAGCA Uncertain significance (Jul 15, 2022)1982646
7-97006052-GCAGCAGCAGCAGCAGCAGCAGCAA-G Uncertain significance (Jun 18, 2022)1463454
7-97006052-G-GCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAA Uncertain significance (Jul 14, 2023)2867465
7-97006052-G-GCAGCAGCAGCAGCAGCAGCAGCAA not specified Conflicting classifications of pathogenicity (Dec 06, 2023)1301676
7-97006055-GCAGCAGCAGCAGCAGCAGCAA-G Uncertain significance (Sep 05, 2023)1498979
7-97006055-G-GCAGCAGCAGCAGCAGCAGCAA Uncertain significance (Nov 30, 2022)2697545
7-97006058-GCAGCAGCAGCAGCAGCAA-G Uncertain significance (Aug 04, 2023)1365121
7-97006061-GCAGCAGCAGCAGCAA-G Uncertain significance (Aug 17, 2023)1501223
7-97006064-G-GCAGCAGCAGCAA Uncertain significance (Jun 22, 2023)2894545
7-97006070-G-A DLX6-related disorder Likely benign (Dec 08, 2021)2041446
7-97006076-A-G Likely benign (Apr 10, 2023)2046086
7-97006076-A-ACAG DLX6-related disorder Uncertain significance (Apr 09, 2023)2053894
7-97006076-A-ACAGCAGCAG Uncertain significance (Aug 03, 2023)2887892
7-97006079-G-A Likely benign (Mar 01, 2023)2657693
7-97006080-C-G Uncertain significance (Nov 15, 2023)2957975
7-97006081-AGCAGCAGCAGCAGCAGCAACAGCAACA-C Uncertain significance (Dec 08, 2021)1972465
7-97006082-G-A Likely benign (Dec 07, 2023)1561703

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DLX6protein_codingprotein_codingENST00000518156 35492
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9210.078600000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.171051450.7260.000006821888
Missense in Polyphen2761.8340.43665747
Synonymous-2.277957.21.380.00000276537
Loss of Function3.02112.50.07975.45e-7135

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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