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 (43 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			43 clinvar		1 clinvar	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	2

Loading clinvar variants...

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