DBX2

developing brain homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 12:45014671-45051099

Links

ENSG00000185610 ∙ NCBI:440097 ∙ ∙ HGNC:33186 ∙ Uniprot:Q6ZNG2 ∙ 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 DBX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBX2 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in DBX2

This is a list of pathogenic ClinVar variants found in the DBX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-45016471-T-C		not specified	Uncertain significance (Jan 22, 2024)
12-45016505-C-T			Benign (Dec 31, 2019)
12-45016506-C-T		not specified	Uncertain significance (Mar 07, 2023)
12-45016513-G-A		not specified	Uncertain significance (Mar 15, 2024)
12-45023760-T-C		not specified	Uncertain significance (Jan 23, 2024)
12-45023807-T-C		not specified	Uncertain significance (Jan 06, 2023)
12-45023835-T-C		not specified	Uncertain significance (Nov 08, 2021)
12-45036043-G-A		not specified	Uncertain significance (Jul 05, 2023)
12-45036045-C-T		not specified	Uncertain significance (Feb 26, 2024)
12-45036046-G-A		not specified	Uncertain significance (Dec 21, 2023)
12-45036061-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-45036070-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-45036077-G-C		not specified	Uncertain significance (Oct 05, 2023)
12-45036087-G-T		not specified	Uncertain significance (Feb 15, 2023)
12-45050536-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-45050539-T-C		not specified	Uncertain significance (Jan 23, 2024)
12-45050558-C-T		not specified	Uncertain significance (Apr 09, 2024)
12-45050589-G-C		not specified	Uncertain significance (Aug 17, 2021)
12-45050617-G-A		not specified	Uncertain significance (May 29, 2024)
12-45050636-G-C		not specified	Uncertain significance (Jun 06, 2023)
12-45050744-G-C		not specified	Uncertain significance (May 23, 2023)
12-45050746-T-C		not specified	Likely benign (Aug 15, 2023)
12-45050749-T-G		not specified	Uncertain significance (Jun 11, 2021)
12-45050756-C-G		not specified	Likely benign (Jun 11, 2021)
12-45050827-A-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBX2	protein_coding	protein_coding	ENST00000332700	4	36428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000606	0.469	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.127	164	160	1.03	0.00000805	2085
Missense in Polyphen		30	39.821	0.75337		564
Synonymous	-2.48	92	66.3	1.39	0.00000345	714
Loss of Function	0.594	9	11.1	0.808	5.63e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.0000560	0.0000544
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0932

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.198
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0918

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbx2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding