MEIS1
protein-codingMeis homeobox 1, the group of TALE class homeoboxes and pseudogenes
Gene summary
Homeobox genes, of which the most well-characterized category is represented by the HOX genes, play a crucial role in normal development. In addition, several homeoproteins are involved in neoplasia. This gene encodes a homeobox protein belonging to the TALE ('three amino acid loop extension') family of homeodomain-containing proteins. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~140.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0002049
Submitter: ClinGen
*MEIS1* was first reported in relation to congenital thrombocytopenia in 2022 (Steinberg-Shemer et al., 2022 PMID: 35130804). *MEIS1* is a homeobox gene that acts as a transcriptional regulator of genes involved in embryonic development, cell differentiation, hematopoiesis, and neural development. To date, there has been one report of a de novo heterozygous variant in *MEIS1* causing severe congenital thrombocytopenia. Additionally, MEIS1 overexpression is common in leukemias (specifically MLL-fusion-induced leukemia) and is caused by upstream activation of oncogenes interacting with MEIS1, not specific variants in the MEIS1 gene, and is not included in this curation. Evidence supporting this gene-disease curation includes case level data and experimental data. Summary of Case Level Data (1 point): One de novo heterozygous splicing variant (c. 432+5G>C) that has been shown to lead exon skipping and a premature stop codon. This variant as been reported in a single proband. Summary of Experimental Evidence (2.5 points): This gene disease relationship is supported by mouse model systems (Azcoitia et al., 2005 PMID: 15882575; Hisa et al., 2004 PMID: 14713950; Miller et al., 2016 PMID: 26986211), a zebrafish model (Cvejic et al., 2011 PMID: 21048033) and functional alteration in non-patient cells (Wang et al., 2018 PMID: 29358086). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This gene-disease relationship was curated by the ClinGen Hemostasis and Thrombosis (H/T) Gene Curation Expert Panel using Gene Clinical Validity Standard Operating Procedures (SOP), Version 11.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MEIS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002398.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 1 | 4 | ||
| missense | 29 | 29 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 37 | 2 | 1 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002389.1 | 12 | MANE Select | |
| Ensembl | ENSP00000272369.8 | 12 | MANE Select | |
| Ensembl | ENSP00000381518.2 | 11 | Standard | |
| Ensembl | ENSP00000381518.2 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| meis1b | Danio rerio | Structure: thrombocyte Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
- Transcriptional misregulation in cancer - Homo sapiens (human)
- Mesodermal Commitment Pathway
Biological Process
- angiogenesis
- lens morphogenesis in camera-type eye
- locomotory behavior
- megakaryocyte development
- negative regulation of myeloid cell differentiation
Molecular Function
- RNA polymerase II proximal 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
- chromatin binding
Cellular Component
- nucleus
- transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000272369
- Coding exons
- 12
- Length
- 140418
- Individuals with no LoFs
- 124792
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 124794
- p
- 0.00000801
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.30 | 86 | 226 | 0.381 | 0.0000113 | 2577 |
| Missense (PolyPhen) | 5 | 49.535 | 0.10094 | 607 | ||
| Synonymous | -0.109 | 79 | 77.8 | 1.02 | 0.00000426 | 683 |
| Loss of Function | 4.34 | 0 | 21.9 | 0.00 | 0.00000102 | 269 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a transcriptional regulator of PAX6. Acts as a transcriptional activator of PF4 in complex with PBX1 or PBX2. Required for hematopoiesis, megakaryocyte lineage development and vascular patterning. May function as a cofactor for HOXA7 and HOXA9 in the induction of myeloid leukemias. {ECO:0000269|PubMed:12609849}.;
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- LoFtool
- 0.351
- RVIS EVS
- -0.32
- RVIS percentile EVS
- 31.46
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |