GBX2

gastrulation brain homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:236165235-236168386

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.

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.

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			16		1	17
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	0	2

Variants in GBX2

This is a list of pathogenic ClinVar variants found in the GBX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-236166032-G-T		not specified	Uncertain significance (Nov 01, 2021)
2-236166184-C-T			Benign (Jul 23, 2018)
2-236166192-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-236166232-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
2-236166252-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-236166255-C-A		not specified	Uncertain significance (Mar 19, 2024)
2-236166260-C-G		not specified	Uncertain significance (Oct 05, 2023)
2-236166276-C-T		not specified	Uncertain significance (Jan 19, 2024)
2-236167550-G-A		not specified	Uncertain significance (Apr 20, 2023)
2-236167565-C-T		not specified	Uncertain significance (May 08, 2024)
2-236167566-C-G		not specified	Uncertain significance (Jun 18, 2021)
2-236167568-C-A		not specified	Uncertain significance (Jun 10, 2022)
2-236167612-C-G			Benign (Jul 23, 2018)
2-236167643-C-A		not specified	Uncertain significance (Jan 10, 2023)
2-236167657-C-T		not specified	Uncertain significance (Jun 16, 2024)
2-236167678-C-T		not specified	Uncertain significance (May 17, 2023)
2-236167682-C-G		not specified	Uncertain significance (May 27, 2022)
2-236167724-A-G		not specified	Uncertain significance (Jun 17, 2022)
2-236167754-G-T		not specified	Uncertain significance (Dec 14, 2023)
2-236167808-A-G		not specified	Uncertain significance (Nov 09, 2023)
2-236167821-G-C		not specified	Uncertain significance (Aug 17, 2022)
2-236167959-A-G		not specified	Uncertain significance (Jun 10, 2022)

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
0.713	0.284	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

Haploinsufficiency Scores

• pHI: 0.799
• hipred: Y
• hipred_score: 0.670
• ghis: 0.436

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

Mouse Genome Informatics

• Gene name: Gbx2
• Phenotype: craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype; 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); 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); hematopoietic system phenotype; growth/size/body region phenotype; vision/eye 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); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype

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