MIXL1
Mix paired-like homeobox, the group of PRD class homeoboxes and pseudogenes
Basic information
Region (hg38): 1:226223618-226227060
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 MIXL1 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 | 18 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 1 | 0 |
Variants in MIXL1
This is a list of pathogenic ClinVar variants found in the MIXL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-226223701-G-A | not specified | Uncertain significance (Nov 13, 2023) | ||
| 1-226223743-G-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-226223757-G-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 1-226223773-C-A | not specified | Uncertain significance (Oct 13, 2023) | ||
| 1-226223830-C-T | not specified | Uncertain significance (Jan 03, 2022) | ||
| 1-226223832-A-C | not specified | Likely benign (Sep 16, 2021) | ||
| 1-226223851-G-C | not specified | Uncertain significance (Jan 24, 2024) | ||
| 1-226223871-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 1-226223887-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-226223908-C-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 1-226223961-A-G | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-226223970-C-A | not specified | Uncertain significance (Sep 30, 2022) | ||
| 1-226223985-G-C | not specified | Uncertain significance (Jun 29, 2022) | ||
| 1-226225600-G-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 1-226225669-G-A | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-226225713-A-C | not specified | Uncertain significance (Apr 17, 2024) | ||
| 1-226225724-T-C | not specified | Uncertain significance (May 11, 2022) | ||
| 1-226225733-G-T | not specified | Uncertain significance (Jan 24, 2023) | ||
| 1-226225741-C-G | not specified | Uncertain significance (Mar 14, 2023) | ||
| 1-226225745-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-226225807-T-G | not specified | Uncertain significance (May 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MIXL1 | protein_coding | protein_coding | ENST00000366810 | 2 | 3437 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0171 | 0.730 | 125723 | 0 | 19 | 125742 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.426 | 86 | 97.9 | 0.879 | 0.00000516 | 1434 |
| Missense in Polyphen | 24 | 34.012 | 0.70564 | 411 | ||
| Synonymous | 0.974 | 36 | 44.2 | 0.814 | 0.00000234 | 531 |
| Loss of Function | 0.740 | 3 | 4.74 | 0.633 | 2.02e-7 | 61 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation. Required for efficient differentiation of cells from the primitive streak stage to blood, by acting early in the recruitment and/or expansion of mesodermal progenitors to the hemangioblastic and hematopoietic lineages. Also involved in the morphogenesis of the heart and the gut during embryogenesis. Acts as a negative regulator of brachyury expression (By similarity). {ECO:0000250}.;
- Pathway
- Adipogenesis;Cardiac Progenitor Differentiation;Endoderm Differentiation;Mesodermal Commitment Pathway
(Consensus)
Recessive Scores
- pRec
- 0.249
Haploinsufficiency Scores
- pHI
- 0.178
- hipred
- N
- hipred_score
- 0.220
- ghis
- 0.475
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mixl1
- Phenotype
- growth/size/body region phenotype; embryo 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); digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- mixl1
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- hematopoietic progenitor cell differentiation;gastrulation;endoderm development;heart development;hemopoiesis;endodermal cell differentiation;cell migration involved in gastrulation;positive regulation of transcription by RNA polymerase II;digestive tract development;negative regulation of hematopoietic progenitor cell differentiation;positive regulation of mesoderm development
- Cellular component
- nuclear chromatin;nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;RNA polymerase II transcription factor binding;RNA polymerase II repressing transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;protein homodimerization activity