DLX3

distal-less homeobox 3, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 17:49990005-49995224

Links

ENSG00000064195NCBI:1747OMIM:600525HGNC:2916Uniprot:O60479AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • tricho-dento-osseous syndrome (Moderate), mode of inheritance: AD
  • hypomaturation-hypoplastic amelogenesis imperfecta with taurodontism (Limited), mode of inheritance: AD
  • tricho-dento-osseous syndrome (Supportive), mode of inheritance: AD
  • hypomaturation-hypoplastic amelogenesis imperfecta with taurodontism (Supportive), mode of inheritance: AD
  • tricho-dento-osseous syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Trichodontoosseous syndrome; Amelogenesis imperfecta, type IVADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Dental; Dermatologic; Musculoskeletal9467018; 9783705; 10466415; 15666299; 18203197; 18362318; 18492670; 19608154; 21252474

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DLX3 gene.

  • not_provided (99 variants)
  • Inborn_genetic_diseases (40 variants)
  • Hypomaturation-hypoplastic_amelogenesis_imperfecta_with_taurodontism (24 variants)
  • Tricho-dento-osseous_syndrome (7 variants)
  • DLX3-related_disorder (6 variants)
  • not_specified (3 variants)
  • Amelogenesis_Imperfecta,_Dominant (1 variants)
  • Peripheral_pulmonary_artery_stenosis (1 variants)
  • Amelogenesis_imperfecta (1 variants)
  • Uterine_leiomyoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005220.3. 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
37
clinvar
2
clinvar
39
missense
1
clinvar
4
clinvar
70
clinvar
6
clinvar
4
clinvar
85
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
0
Total 2 7 71 43 6

Highest pathogenic variant AF is 0.0000111518

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DLX3protein_codingprotein_codingENST00000434704 35220
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002550.9381257060151257210.0000597
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9571341690.7930.000009041822
Missense in Polyphen4157.0230.719567
Synonymous0.6597380.50.9070.00000452598
Loss of Function1.65612.20.4915.29e-7130

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00008810.0000879
Middle Eastern0.00005450.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Likely to play a regulatory role in the development of the ventral forebrain. May play a role in craniofacial patterning and morphogenesis.;
Disease
DISEASE: Trichodentoosseous syndrome (TDO) [MIM:190320]: An autosomal dominant disease characterized by curly kinky hair at birth, enamel hypoplasia, taurodontism, thickening of cortical bones and variable expression of craniofacial morphology. {ECO:0000269|PubMed:9467018}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Amelogenesis imperfecta 4 (AI4) [MIM:104510]: An autosomal dominant defect of enamel formation associated with enlarged pulp chambers. Enamel is thin, teeth are small and widely spaced. {ECO:0000269|PubMed:15666299}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.212

Intolerance Scores

loftool
0.195
rvis_EVS
-0.32
rvis_percentile_EVS
31.69

Haploinsufficiency Scores

pHI
0.524
hipred
Y
hipred_score
0.588
ghis
0.581

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.294

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Dlx3
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); endocrine/exocrine gland phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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);

Zebrafish Information Network

Gene name
dlx3b
Affected structure
otolith
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
blood vessel development;placenta development;regulation of transcription by RNA polymerase II;cell differentiation;epithelial cell differentiation;odontogenesis of dentin-containing tooth;positive regulation of transcription by RNA polymerase II;odontoblast differentiation
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 activator activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding