MEIS1

protein-coding

Meis 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

NM_002398.3

Inheritance

AD

ClinVar variants

U:37B:3

Top phenotype

MEIS1-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr2:66,433,452-66,573,869

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~140.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

thrombocytopeniaLIMITED

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

4 Conditions Cataloged
not specifiedTotal: 26
MEIS1-related disorderTotal: 4
not providedTotal: 3
See casesTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
1
clinvar
4
missense
29
clinvar
29
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total00372140
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002398.3RefSeqNP_002389.112MANE Select
ENST00000272369.14EnsemblENSP00000272369.812MANE Select
ENST00000398506.6EnsemblENSP00000381518.211Standard
ENST00000398506.7EnsemblENSP00000381518.211Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
meis1bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.30862260.3810.00001132577
Missense (PolyPhen)549.5350.10094607
Synonymous-0.1097977.81.020.00000426683
Loss of Function4.34021.90.000.00000102269

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00013rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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