DLX6

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

Basic information

Region (hg38): 7:97005553-97011040

Links

ENSG00000006377 ∙ NCBI:1750 ∙ OMIM:600030 ∙ HGNC:2919 ∙ Uniprot:P56179 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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				16	3	19
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel			31	2	4	37
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	4	7
Total	0	0	53	23	11

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)
7-97006025-G-T			Likely benign (Feb 01, 2024)
7-97006028-C-T			Benign (Jul 30, 2024)
7-97006051-GGCA-G			Benign (Sep 06, 2024)
7-97006051-GGCAGCA-G		DLX6-related disorder	Uncertain significance (Nov 19, 2024)
7-97006051-GGCAGCAGCA-G			Uncertain significance (Mar 02, 2023)
7-97006051-GGCAGCAGCAGCA-G			Uncertain significance (Mar 11, 2024)
7-97006051-G-GGCA		DLX6-related disorder	Uncertain significance (May 17, 2024)
7-97006051-G-GGCAGCA			Uncertain significance (Oct 09, 2024)
7-97006051-G-GGCAGCAGCA			Uncertain significance (Dec 09, 2024)
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-GCAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAA			Uncertain significance (Aug 31, 2024)
7-97006052-G-GCAGCAGCAGCAGCAGCAGCAGCAA		not specified	Conflicting classifications of pathogenicity (Jan 06, 2025)
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)
7-97006058-G-GCAGCAGCAGCAA			Uncertain significance (Jul 22, 2024)
7-97006061-G-T			Uncertain significance (Jan 06, 2025)
7-97006061-GCAGCAGCAGCAGCAA-G			Uncertain significance (Aug 17, 2023)
7-97006064-G-GCAGCAGCAGCAA			Uncertain significance (Jun 22, 2023)
7-97006066-A-G			Uncertain significance (Mar 18, 2024)
7-97006070-G-A		DLX6-related disorder	Likely benign (Dec 08, 2021)

GnomAD

Source: gnomAD

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: 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

	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