DLX2

distal-less homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 2:172099438-172102900

Links

ENSG00000115844 ∙ NCBI:1746 ∙ OMIM:126255 ∙ HGNC:2915 ∙ Uniprot:Q07687 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DLX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLX2 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				1	2	3
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	2

Variants in DLX2

This is a list of pathogenic ClinVar variants found in the DLX2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-172100575-C-G		not specified	Uncertain significance (Aug 20, 2024)
2-172100586-T-C		not specified	Uncertain significance (Sep 26, 2024)
2-172100638-G-T		not specified	Uncertain significance (Dec 02, 2021)
2-172100639-C-A			Likely benign (Aug 08, 2018)
2-172100650-G-T		not specified	Uncertain significance (Jul 12, 2023)
2-172100658-G-A		not specified	Uncertain significance (Mar 25, 2022)
2-172100668-C-T		not specified	Uncertain significance (Nov 13, 2024)
2-172100677-G-C		not specified	Uncertain significance (Aug 05, 2024)
2-172100682-T-A		not specified	Uncertain significance (Apr 09, 2024)
2-172100737-A-C		not specified	Uncertain significance (Nov 29, 2021)
2-172100743-C-A		not specified	Uncertain significance (Feb 12, 2024)
2-172100743-C-G		not specified	Uncertain significance (Jan 23, 2023)
2-172100759-A-T		not specified	Uncertain significance (May 31, 2023)
2-172100790-T-G		not specified	Uncertain significance (Nov 13, 2023)
2-172100793-G-T		not specified	Uncertain significance (Sep 27, 2024)
2-172100815-C-T		not specified	Uncertain significance (Jul 26, 2024)
2-172100830-G-C		not specified	Uncertain significance (Jul 20, 2021)
2-172100880-G-A		not specified	Uncertain significance (Nov 10, 2024)
2-172100890-C-T		not specified	Uncertain significance (May 18, 2022)
2-172101479-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-172101552-C-A			Benign (May 03, 2018)
2-172101593-C-T		not specified	Uncertain significance (Jan 17, 2023)
2-172101608-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-172102261-T-C		not specified	Uncertain significance (Oct 08, 2024)
2-172102267-T-A		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLX2	protein_coding	protein_coding	ENST00000234198	3	3462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0215	125703	0	2	125705	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.949	141	176	0.799	0.00000799	2090
Missense in Polyphen		26	47.467	0.54775		517
Synonymous	0.281	76	79.2	0.960	0.00000382	683
Loss of Function	3.18	0	11.8	0.00	5.02e-7	129

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional activator. Plays a role in terminal differentiation of interneurons, such as amacrine and bipolar cells in the developing retina. Likely to play a regulatory role in the development of the ventral forebrain. May play a role in craniofacial patterning and morphogenesis. {ECO:0000250|UniProtKB:P40764}.
• Pathway: Preimplantation Embryo;Olfactory bulb development and olfactory learning;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.189
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.895
• hipred: Y
• hipred_score: 0.806
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dlx2
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); 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); 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); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; skeleton phenotype; growth/size/body region phenotype; muscle phenotype; craniofacial phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: dlx2a
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;brain development;proximal/distal pattern formation;subpallium development;hippocampus development;olfactory bulb development;regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment;cerebral cortex GABAergic interneuron fate commitment;cell differentiation;odontogenesis of dentin-containing tooth;positive regulation of cell differentiation;negative regulation of Notch signaling pathway;positive regulation of transcription by RNA polymerase II;negative regulation of photoreceptor cell differentiation;embryonic cranial skeleton morphogenesis;negative regulation of oligodendrocyte differentiation;branching morphogenesis of a nerve;cartilage development;positive regulation of amacrine cell differentiation
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;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;chromatin binding;DNA-binding transcription factor activity;single-stranded RNA binding;protein binding;sequence-specific DNA binding