Human Gene Module / Chromosome 15 / MEIS2

MEIS2Meis homeobox 2

Score
1
High Confidence Criteria 1.1
Autism Reports / Total Reports
2 / 7
Rare Variants / Common Variants
21 / 0
Aliases
MEIS2, CPCMR,  HsT18361,  MRG1
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Syndromic
Chromosome Band
15q14
Associated Disorders
ASD
Relevance to Autism

Heterozygous mutations in the MEIS2 gene, frequently in the form of 15q14 microdeletions, are responsible for cleft palate, cardiac defects, and mental retardation (CPCMR; OMIM 600987). A de novo in-frame deletion variant in the MEIS2 gene was identified in a female patient diagnosed with ASD in Louw et al., 2015. A de novo 15q14 microdeletion involving MEIS2 was observed in a patient presenting with autistic behavior in Shimojima et al., 2017. Douglas et al., 2018 reported four individuals with de novo predicted damaging missense variants in the MEIS2 gene; in addition to features resembling those observed in patients with 15q14 deletions, three of the individuals in Douglas et al., 2018 presented with autism or ASD.

Molecular Function

This gene encodes a homeobox protein belonging to the TALE ('three amino acid loop extension') family of homeodomain-containing proteins. TALE homeobox proteins are highly conserved transcription regulators, and several members have been shown to be essential contributors to developmental programs.

Reports related to MEIS2 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary MEIS2 involvement in cardiac development, cleft palate, and intellectual disability. Louw JJ , et al. (2015) No ASD
2 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
3 Support A 15q14 microdeletion involving MEIS2 identified in a patient with autism spectrum disorder. Shimojima K , et al. (2017) No Autistic behavior
4 Recent Recommendation De novo missense variants in MEIS2 recapitulate the microdeletion phenotype of cardiac and palate abnormalities, developmental delay, intellectual ... Douglas G , et al. (2018) No ASD
5 Support Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability. Verheije R , et al. (2018) No ASD
6 Support Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with develop... Schluth-Bolard C , et al. (2019) No Microcephaly
7 Support Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes Feliciano P et al. (2019) Yes -
Rare Variants   (21)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown - - 30291340 Verheije R , et al. (2018)
- - copy_number_loss De novo NA - 30291340 Verheije R , et al. (2018)
- - copy_number_loss De novo NA - 28736618 Shimojima K , et al. (2017)
- - translocation De novo NA - 30923172 Schluth-Bolard C , et al. (2019)
- - copy_number_loss Unknown Not maternal - 30291340 Verheije R , et al. (2018)
c.639+1G>A - splice_site_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.640-2A>G - splice_site_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.978-2A>G - splice_site_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.829C>T p.Gln277Ter stop_gained De novo NA - 30291340 Verheije R , et al. (2018)
c.978G>A p.Trp326Ter stop_gained De novo NA - 30291340 Verheije R , et al. (2018)
c.520C>T p.Arg174Ter stop_gained De novo NA - 31452935 Feliciano P et al. (2019)
c.905C>T p.Pro302Leu missense_variant De novo NA - 30055086 Douglas G , et al. (2018)
c.965A>T p.Gln322Leu missense_variant De novo NA - 30055086 Douglas G , et al. (2018)
c.992G>A p.Arg331Lys missense_variant De novo NA - 30055086 Douglas G , et al. (2018)
c.1004T>C p.Val335Ala missense_variant De novo NA - 30055086 Douglas G , et al. (2018)
c.998G>A p.Arg333Lys missense_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.324_326del p.Ala109del inframe_deletion De novo NA - 25712757 Louw JJ , et al. (2015)
c.956C>T p.Thr319Ile missense_variant De novo NA Multiplex 28263302 C Yuen RK et al. (2017)
c.383del p.Lys128SerfsTer19 frameshift_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.868dup p.Ile290AsnfsTer40 frameshift_variant De novo NA - 30291340 Verheije R , et al. (2018)
c.934_937del p.Leu312ArgfsTer11 frameshift_variant De novo NA - 30291340 Verheije R , et al. (2018)
Common Variants  

No common variants reported.

SFARI Gene score
1

High Confidence

Heterozygous mutations in the MEIS2 gene, frequently in the form of 15q14 microdeletions, are responsible for cleft palate, cardiac defects, and mental retardation (CPCMR; OMIM 600987). A de novo in-frame deletion variant in the MEIS2 gene was identified in a female patient diagnosed with ASD in Louw et al., 2015. A de novo 15q14 microdeletion involving MEIS2 was observed in a patient presenting with autistic behavior in Shimojima et al., 2017. Douglas et al., 2018 reported four individuals with de novo predicted damaging missense variants in the MEIS2 gene; in addition to features resembling those observed in patients with 15q14 deletions, three of the individuals in Douglas et al., 2018 presented with autism or ASD. Verheije et al., 2018 collected 23 previously reported individuals with either a de novo sequence variant in MEIS2 (9 patients) or a 15q14 microdeletion affecting MEIS2 (14 patients) and determined that autism was observed in 2/9 patients with a de novo MEIS2 sequence variants and in 3/14 patients with a 15q14 microdeletion affecting MEIS2.

Score Delta: Score remained at S

1

High Confidence

See all Category 1 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

10/1/2019
S
icon
1

Increased from S to 1

New Scoring Scheme
Description

Heterozygous mutations in the MEIS2 gene, frequently in the form of 15q14 microdeletions, are responsible for cleft palate, cardiac defects, and mental retardation (CPCMR; OMIM 600987). A de novo in-frame deletion variant in the MEIS2 gene was identified in a female patient diagnosed with ASD in Louw et al., 2015. A de novo 15q14 microdeletion involving MEIS2 was observed in a patient presenting with autistic behavior in Shimojima et al., 2017. Douglas et al., 2018 reported four individuals with de novo predicted damaging missense variants in the MEIS2 gene; in addition to features resembling those observed in patients with 15q14 deletions, three of the individuals in Douglas et al., 2018 presented with autism or ASD. Verheije et al., 2018 collected 23 previously reported individuals with either a de novo sequence variant in MEIS2 (9 patients) or a 15q14 microdeletion affecting MEIS2 (14 patients) and determined that autism was observed in 2/9 patients with a de novo MEIS2 sequence variants and in 3/14 patients with a 15q14 microdeletion affecting MEIS2.

4/1/2019
S
icon
S

Increased from S to S

Description

Heterozygous mutations in the MEIS2 gene, frequently in the form of 15q14 microdeletions, are responsible for cleft palate, cardiac defects, and mental retardation (CPCMR; OMIM 600987). A de novo in-frame deletion variant in the MEIS2 gene was identified in a female patient diagnosed with ASD in Louw et al., 2015. A de novo 15q14 microdeletion involving MEIS2 was observed in a patient presenting with autistic behavior in Shimojima et al., 2017. Douglas et al., 2018 reported four individuals with de novo predicted damaging missense variants in the MEIS2 gene; in addition to features resembling those observed in patients with 15q14 deletions, three of the individuals in Douglas et al., 2018 presented with autism or ASD. Verheije et al., 2018 collected 23 previously reported individuals with either a de novo sequence variant in MEIS2 (9 patients) or a 15q14 microdeletion affecting MEIS2 (14 patients) and determined that autism was observed in 2/9 patients with a de novo MEIS2 sequence variants and in 3/14 patients with a 15q14 microdeletion affecting MEIS2.

10/1/2018
S
icon
S

Increased from S to S

Description

Heterozygous mutations in the MEIS2 gene, frequently in the form of 15q14 microdeletions, are responsible for cleft palate, cardiac defects, and mental retardation (CPCMR; OMIM 600987). A de novo in-frame deletion variant in the MEIS2 gene was identified in a female patient diagnosed with ASD in Louw et al., 2015. A de novo 15q14 microdeletion involving MEIS2 was observed in a patient presenting with autistic behavior in Shimojima et al., 2017. Douglas et al., 2018 reported four individuals with de novo predicted damaging missense variants in the MEIS2 gene; in addition to features resembling those observed in patients with 15q14 deletions, three of the individuals in Douglas et al., 2018 presented with autism or ASD. Verheije et al., 2018 collected 23 previously reported individuals with either a de novo sequence variant in MEIS2 (9 patients) or a 15q14 microdeletion affecting MEIS2 (14 patients) and determined that autism was observed in 2/9 patients with a de novo MEIS2 sequence variants and in 3/14 patients with a 15q14 microdeletion affecting MEIS2.

Krishnan Probability Score

Score 0.54359785644328

Ranking 1420/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99425495510655

Ranking 1586/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.93499763783444

Ranking 12740/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.083167833905367

Ranking 6472/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.
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