DBX1

developing brain homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 11:20156155-20160475

Links

ENSG00000109851 ∙ NCBI:120237 ∙ OMIM:619830 ∙ HGNC:33185 ∙ Uniprot:A6NMT0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DBX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBX1 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			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in DBX1

This is a list of pathogenic ClinVar variants found in the DBX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-20156273-A-G		not specified	Uncertain significance (Feb 26, 2024)
11-20156275-T-G		not specified	Uncertain significance (Nov 09, 2024)
11-20156306-C-T		not specified	Uncertain significance (Dec 13, 2023)
11-20156315-G-T		not specified	Uncertain significance (Dec 17, 2023)
11-20156327-C-G		not specified	Uncertain significance (Jun 03, 2022)
11-20156419-T-G		not specified	Uncertain significance (Feb 14, 2023)
11-20156428-G-T		not specified	Uncertain significance (Aug 16, 2022)
11-20156434-T-C		not specified	Uncertain significance (Aug 02, 2022)
11-20156480-G-A		not specified	Uncertain significance (Jun 16, 2023)
11-20156509-G-C		not specified	Uncertain significance (May 03, 2023)
11-20156511-C-T			Likely benign (Jun 01, 2022)
11-20156512-A-C		not specified	Uncertain significance (Feb 02, 2022)
11-20157198-G-T		not specified	Uncertain significance (Sep 06, 2022)
11-20159251-A-C		not specified	Uncertain significance (Aug 01, 2024)
11-20159254-T-A		not specified	Uncertain significance (Jan 06, 2023)
11-20159281-C-G		not specified	Uncertain significance (May 14, 2024)
11-20159975-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-20160071-G-A		not specified	Uncertain significance (Oct 24, 2024)
11-20160086-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-20160159-G-T		not specified	Uncertain significance (Aug 20, 2024)
11-20160314-G-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBX1	protein_coding	protein_coding	ENST00000227256	4	4459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0610	0.924	125709	0	23	125732	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.123	225	220	1.02	0.00000995	2400
Missense in Polyphen		70	81.627	0.85756		929
Synonymous	-0.984	116	103	1.12	0.00000484	856
Loss of Function	2.13	4	11.9	0.336	5.29e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000237	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could have a role in patterning the central nervous system during embryogenesis. Has a key role in regulating the distinct phenotypic features that distinguish two major classes of ventral interneurons, V0 and V1 neurons. Regulates the transcription factor profile, neurotransmitter phenotype, intraspinal migratory path and axonal trajectory of V0 neurons, features that differentiate them from an adjacent set of V1 neurons (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.634

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbx1
• 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell differentiation in spinal cord;ventral spinal cord interneuron specification
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding