GBX2

gastrulation brain homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:236165236-236168386

Links

ENSG00000168505 ∙ NCBI:2637 ∙ OMIM:601135 ∙ HGNC:4186 ∙ Uniprot:P52951 ∙ 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 GBX2 gene.

• not_specified (48 variants)
• not_provided (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001485.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			48		1	49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	1	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBX2	protein_coding	protein_coding	ENST00000306318	2	3134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125660	0	3	125663	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	134	188	0.712	0.00000961	2221
Missense in Polyphen		46	75.857	0.6064		865
Synonymous	1.62	67	86.1	0.778	0.00000448	731
Loss of Function	2.37	1	8.43	0.119	3.73e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transcription factor for cell pluripotency and differentiation in the embryo.
• Pathway: Neural Crest Differentiation;Dopaminergic Neurogenesis (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.0466
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.576

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: gbx2
• Affected structure: rhombomere 4
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: branching involved in blood vessel morphogenesis;neural crest cell migration;nervous system development;axon guidance;cerebellum development;midbrain-hindbrain boundary morphogenesis;rhombomere 2 development;thalamus development;forebrain neuron development;cerebellar granule cell precursor proliferation;hindbrain development;inner ear morphogenesis;positive regulation of transcription by RNA polymerase II;autonomic nervous system development;regulation of nervous system development
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity