MEIS1
Meis homeobox 1, the group of TALE class homeoboxes and pseudogenes
Basic information
Region (hg38): 2:66433451-66573869
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 MEIS1 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 | 2 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 1 |
Variants in MEIS1
This is a list of pathogenic ClinVar variants found in the MEIS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-66437762-G-A | not specified | Uncertain significance (Oct 27, 2022) | ||
| 2-66437793-G-A | not specified | Uncertain significance (Jun 27, 2022) | ||
| 2-66437815-A-C | MEIS1-related disorder | Likely benign (Mar 28, 2019) | ||
| 2-66437836-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 2-66437851-C-T | not specified | Uncertain significance (May 01, 2024) | ||
| 2-66437931-C-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 2-66441435-T-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 2-66442986-A-G | not specified | Uncertain significance (Dec 17, 2023) | ||
| 2-66568665-A-G | See cases | Uncertain significance (Sep 24, 2019) | ||
| 2-66568707-G-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 2-66568723-G-A | not specified | Uncertain significance (May 10, 2024) | ||
| 2-66568725-C-T | Benign (Mar 30, 2018) | |||
| 2-66568750-G-A | not specified | Uncertain significance (Jun 18, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MEIS1 | protein_coding | protein_coding | ENST00000272369 | 12 | 140418 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000488 | 124792 | 0 | 2 | 124794 | 0.00000801 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.30 | 86 | 226 | 0.381 | 0.0000113 | 2577 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000131 | 0.000129 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Mesodermal Commitment Pathway
(Consensus)
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- loftool
- 0.351
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.841
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Meis1
- Phenotype
- 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); cellular phenotype; vision/eye 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); hematopoietic system phenotype; 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); liver/biliary system phenotype; respiratory system phenotype; renal/urinary system 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);
Zebrafish Information Network
- Gene name
- meis1b
- Affected structure
- thrombocyte
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- angiogenesis;lens morphogenesis in camera-type eye;locomotory behavior;megakaryocyte development;negative regulation of myeloid cell differentiation;negative regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;negative regulation of cardiac muscle cell proliferation;definitive hemopoiesis
- Cellular component
- nucleus;transcription factor complex
- 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;protein binding;protein heterodimerization activity