BARX1
Basic information
Region (hg38): 9:93951626-93955355
Links
Phenotypes
GenCC
Source:
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 BARX1 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in BARX1
This is a list of pathogenic ClinVar variants found in the BARX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-93952217-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
| 9-93952247-G-C | not specified | Uncertain significance (Feb 14, 2023) | ||
| 9-93952265-T-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 9-93952926-T-G | not specified | Uncertain significance (Jan 30, 2024) | ||
| 9-93952958-C-G | not specified | Uncertain significance (Sep 06, 2022) | ||
| 9-93953044-G-A | not specified | Uncertain significance (Mar 03, 2022) | ||
| 9-93953077-C-T | not specified | Uncertain significance (Mar 11, 2022) | ||
| 9-93954971-A-C | not specified | Uncertain significance (Dec 30, 2023) | ||
| 9-93954974-T-C | not specified | Uncertain significance (Mar 22, 2023) | ||
| 9-93954983-T-G | not specified | Uncertain significance (Aug 06, 2021) | ||
| 9-93955013-G-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 9-93955014-C-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 9-93955082-C-T | not specified | Uncertain significance (May 23, 2023) | ||
| 9-93955092-C-G | not specified | Uncertain significance (Dec 03, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BARX1 | protein_coding | protein_coding | ENST00000253968 | 4 | 3750 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.586 | 0.405 | 125648 | 0 | 1 | 125649 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.07 | 75 | 106 | 0.708 | 0.00000472 | 1567 |
| Missense in Polyphen | 31 | 46.832 | 0.66194 | 625 | ||
| Synonymous | 0.166 | 49 | 50.5 | 0.970 | 0.00000231 | 540 |
| Loss of Function | 2.09 | 1 | 6.95 | 0.144 | 2.94e-7 | 104 |
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) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity (By similarity). Binds to a regulatory module of the NCAM promoter. {ECO:0000250, ECO:0000269|PubMed:9804553}.;
Recessive Scores
- pRec
- 0.178
Haploinsufficiency Scores
- pHI
- 0.200
- hipred
- Y
- hipred_score
- 0.634
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.875
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Barx1
- Phenotype
- cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary 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);
Zebrafish Information Network
- Gene name
- barx1
- Affected structure
- chondroblast
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;cell-cell signaling;tissue development;anterior/posterior pattern specification;negative regulation of Wnt signaling pathway;epithelial cell differentiation;positive regulation of transcription by RNA polymerase II;animal organ development;spleen development;digestive system development
- 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;DNA-binding transcription factor activity