GBX1
gastrulation brain homeobox 1, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 7:151148009-151174745
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBX1 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 | 0 | |||||
| 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 | 0 | 0 |
Variants in GBX1
This is a list of pathogenic ClinVar variants found in the GBX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-151148729-G-T | not specified | Uncertain significance (Sep 12, 2023) | ||
| 7-151148839-T-C | not specified | Uncertain significance (Dec 20, 2023) | ||
| 7-151148891-G-A | not specified | Uncertain significance (Nov 19, 2022) | ||
| 7-151148980-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 7-151148983-T-G | not specified | Uncertain significance (Jul 30, 2023) | ||
| 7-151149133-T-C | not specified | Uncertain significance (Jun 05, 2023) | ||
| 7-151167043-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 7-151167098-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 7-151167196-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 7-151167305-G-A | not specified | Uncertain significance (Jul 30, 2023) | ||
| 7-151167311-C-G | not specified | Uncertain significance (Dec 04, 2023) | ||
| 7-151167392-G-A | not specified | Uncertain significance (Dec 31, 2023) | ||
| 7-151167421-T-A | not specified | Uncertain significance (Jul 19, 2022) | ||
| 7-151167515-C-A | not specified | Uncertain significance (Nov 14, 2023) | ||
| 7-151167530-C-T | not specified | Uncertain significance (Aug 20, 2023) | ||
| 7-151167541-C-G | not specified | Uncertain significance (Apr 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GBX1 | protein_coding | protein_coding | ENST00000297537 | 2 | 26157 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.410 | 0.583 | 124789 | 0 | 2 | 124791 | 0.00000801 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.820 | 160 | 192 | 0.833 | 0.0000111 | 2262 |
| Missense in Polyphen | 44 | 62.762 | 0.70106 | 701 | ||
| Synonymous | 0.491 | 78 | 83.7 | 0.932 | 0.00000460 | 819 |
| Loss of Function | 2.24 | 2 | 9.43 | 0.212 | 5.66e-7 | 103 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000883 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
Haploinsufficiency Scores
- pHI
- 0.412
- hipred
- Y
- hipred_score
- 0.511
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.371
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gbx1
- 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- gbx1
- Affected structure
- midbrain hindbrain boundary neural keel
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;adult walking behavior;proprioception;spinal cord motor neuron differentiation;cerebellum development;hindbrain development;neuron fate commitment;regulation of nervous system development;sensory neuron axon guidance
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;sequence-specific DNA binding