DMBX1

diencephalon/mesencephalon homeobox 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 1:46489835-46516216

Previous symbols: [ "OTX3" ]

Links

ENSG00000197587 ∙ NCBI:127343 ∙ OMIM:607410 ∙ HGNC:19026 ∙ Uniprot:Q8NFW5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DMBX1 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMBX1 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		1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	15	2	0

Variants in DMBX1

This is a list of pathogenic ClinVar variants found in the DMBX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46507089-G-T		not specified	Uncertain significance (Nov 09, 2021)
1-46510466-A-T		not specified	Uncertain significance (Nov 10, 2022)
1-46510555-C-T			Likely benign (Oct 01, 2022)
1-46510953-C-T		6 conditions	Likely pathogenic (Dec 01, 2014)
1-46511045-C-T		DMBX1-related disorder	Benign (Oct 18, 2019)
1-46511052-C-G		not specified	Uncertain significance (Dec 07, 2023)
1-46511089-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-46511156-G-A		DMBX1-related disorder	Likely benign (May 06, 2022)
1-46511176-C-T		not specified	Likely benign (Jan 23, 2023)
1-46511181-C-G		not specified	Uncertain significance (May 06, 2022)
1-46511181-C-T		not specified	Uncertain significance (May 17, 2023)
1-46511199-G-C		DMBX1-related disorder	Benign (May 23, 2019)
1-46511229-A-T		not specified	Uncertain significance (Sep 17, 2021)
1-46512103-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-46512175-C-A		not specified	Uncertain significance (Jul 26, 2022)
1-46512197-G-A		DMBX1-related disorder	Likely benign (Jul 30, 2019)
1-46512211-G-A		not specified	Uncertain significance (May 03, 2023)
1-46512213-G-T		not specified	Uncertain significance (Aug 04, 2021)
1-46512214-G-C		DMBX1-related disorder	Likely benign (Jun 16, 2022)
1-46512231-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-46512243-G-A		not specified	Uncertain significance (May 11, 2022)
1-46512277-C-T		not specified	Uncertain significance (Dec 03, 2021)
1-46512363-C-T		DMBX1-related disorder	Likely benign (Nov 16, 2019)
1-46512367-C-G		DMBX1-related disorder • not specified	Conflicting classifications of pathogenicity (Dec 13, 2023)
1-46512444-C-T		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMBX1	protein_coding	protein_coding	ENST00000360032	4	7231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.930	0.0704	125727	0	5	125732	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	209	246	0.851	0.0000161	2399
Missense in Polyphen		88	128.37	0.68553		1177
Synonymous	0.175	104	106	0.978	0.00000682	820
Loss of Function	3.06	1	12.9	0.0778	5.48e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional repressor. May repress OTX2-mediated transactivation by forming a heterodimer with OTX2 on the P3C (5'-TAATCCGATTA-3') sequence. Required for brain development (By similarity). {ECO:0000250}.
• Pathway: Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

• pHI: 0.197
• hipred: Y
• hipred_score: 0.738
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0526

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmbx1
• Phenotype: reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: dmbx1b
• Affected structure: optic tectum
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;central nervous system development;brain development;adult feeding behavior;adult locomotory behavior;negative regulation of transcription, DNA-templated;developmental growth
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein homodimerization activity;sequence-specific DNA binding;protein heterodimerization activity