Human Gene Module / Chromosome 16 / CMIP

CMIPc-Maf inducing protein

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 7
Rare Variants / Common Variants
4 / 14
Aliases
CMIP, KIAA1694,  TCMIP
Associated Syndromes
-
Chromosome Band
16q23.2-q23.3
Associated Disorders
DD/NDD, ADHD
Relevance to Autism

Single nucleotide polymorphism (SNP) array analysis showed a de novo 280kb deletion on chromosome 16q23.2 involving the CMIP gene in a girl with ASD and developmental delay (Van der Aa et al., 2012). De novo deletions involving the CMIP gene were identified in two additional patients diagnosed with ASD and ADHD and presenting with gastrointestinal issues in Luo et al., 2017.

Molecular Function

This gene encodes a c-Maf inducing protein that plays a role in T-cell signaling pathway. Association studies has shown a possible association between variation in the CMIP gene and nonword repetition ability in specific language impairment (Newbury et al., 2009), as well as between variation in CMIP and dyslexia/reading disability (Scerri et al., 2011).

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to CMIP (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support CMIP and ATP2C2 modulate phonological short-term memory in language impairment Newbury DF , et al. (2009) No -
2 Support DCDC2, KIAA0319 and CMIP are associated with reading-related traits Scerri TS , et al. (2011) No Dyslexia, ADHD
3 Primary Haploinsufficiency of CMIP in a girl with autism spectrum disorder and developmental delay due to a de novo deletion on chromosome 16q23.2 Van der Aa N , et al. (2012) Yes DD
4 Positive Association Language impairment and dyslexia genes influence language skills in children with autism spectrum disorders Eicher JD and Gruen JR (2014) Yes -
5 Support Large-scale discovery of novel genetic causes of developmental disorders Deciphering Developmental Disorders Study (2014) No -
6 Support CMIP haploinsufficiency in two patients with autism spectrum disorder and co-occurring gastrointestinal issues Luo M , et al. (2017) Yes ADHD, DD
7 Support - Soo-Whee Kim et al. (2024) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo - - 28504353 Luo M , et al. (2017)
- - copy_number_loss De novo - Simplex 22689534 Van der Aa N , et al. (2012)
c.1703A>G p.Lys568Arg missense_variant De novo - - 39334436 Soo-Whee Kim et al. (2024)
c.399G>A p.Thr133= synonymous_variant De novo - Unknown 25533962 Deciphering Developmental Disorders Study (2014)
Common Variants   (14)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.145-824C>T;c.427-824C>T;c.211-824C>T;c.319-824C>T;c.-135-824C>T C/T intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.195+7036G>C;c.477+7036G>C;c.261+7036G>C;c.369+7036G>C;c.-85+7036G>C G/C intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.145-2159C>T;c.427-2159C>T;c.211-2159C>T;c.319-2159C>T;c.-135-2159C>T A/G intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.18+21349T>C;c.300+71302T>C;c.-1058T>C;c.-950T>C - intron_variant, 2KB_upstream_varinat - - - 25448322 Eicher JD and Gruen JR (2014)
c.195+10521T>G;c.477+10521T>G;c.261+10521T>G;c.369+10521T>G;c.-85+10521T>G T/G intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.145-824C>T;c.427-824C>T;c.211-824C>T;c.319-824C>T;c.-135-824C>T T(minor allele) intron_variant - - - 21457949 Scerri TS , et al. (2011)
c.196-8360T>C;c.478-8360T>C;c.262-8360T>C;c.370-8360T>C;c.-1705T>C;c.-84-8360T>C C/T intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.145-2159C>T;c.427-2159C>T;c.211-2159C>T;c.319-2159C>T;c.-135-2159C>T T(minor allele) intron_variant - - - 21457949 Scerri TS , et al. (2011)
c.358-1289C>T;c.640-1289C>T;c.424-1289C>T;c.532-1289C>T;c.214-1289C>T;c.79-1289C>T C/T intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.196-12458A>C;c.478-12458A>C;c.262-12458A>C;c.370-12458A>C;c.-84-12458A>C;c.-85+4659A>C - intron_variant - - - 21457949 Scerri TS , et al. (2011)
c.196-12458A>C;c.478-12458A>C;c.262-12458A>C;c.370-12458A>C;c.-84-12458A>C;c.-85+4659A>C C/A intron_variant - - - 19646677 Newbury DF , et al. (2009)
c.300+30147A>C - intron_variant - - - 25448322 Eicher JD and Gruen JR (2014)
c.300+35623A>G - intron_variant - - - 25448322 Eicher JD and Gruen JR (2014)
c.300+11603C>T T/C intron_variant - - - 25448322 Eicher JD and Gruen JR (2014)
SFARI Gene score
2

Strong Candidate

Single nucleotide polymorphism (SNP) array analysis showed a de novo 280kb deletion on chromosome 16q23.2 involving the CMIP gene in a girl with ASD and developmental delay (Van der Aa et al., 2012). De novo deletions involving the CMIP gene were identified in two additional patients diagnosed with ASD and ADHD and presenting with gastrointestinal issues in Luo et al., 2017. Polymorphisms in the CMIP gene have also been shown to associate with specific language impairment (Newbury et al., 2009), reading ability (Scerri et al., 2011), and language skills in ASD cohorts (Eicher and Gruen, 2015).

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 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.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

Single nucleotide polymorphism (SNP) array analysis showed a de novo 280kb deletion on chromosome 16q23.2 involving the CMIP gene in a girl with ASD and developmental delay (Van der Aa et al., 2012). De novo deletions involving the CMIP gene were identified in two additional patients diagnosed with ASD and ADHD and presenting with gastrointestinal issues in Luo et al., 2017. Polymorphisms in the CMIP gene have also been shown to associate with specific language impairment (Newbury et al., 2009), reading ability (Scerri et al., 2011), and language skills in ASD cohorts (Eicher and Gruen, 2015).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Single nucleotide polymorphism (SNP) array analysis showed a de novo 280kb deletion on chromosome 16q23.2 involving the CMIP gene in a girl with ASD and developmental delay (Van der Aa et al., 2012). De novo deletions involving the CMIP gene were identified in two additional patients diagnosed with ASD and ADHD and presenting with gastrointestinal issues in Luo et al., 2017. Polymorphisms in the CMIP gene have also been shown to associate with specific language impairment (Newbury et al., 2009), reading ability (Scerri et al., 2011), and language skills in ASD cohorts (Eicher and Gruen, 2015).

Reports Added
[New Scoring Scheme]
10/1/2017
icon
4

Increased from to 4

Description

Single nucleotide polymorphism (SNP) array analysis showed a de novo 280?kb deletion on chromosome 16q23.2 involving the CMIP gene in a girl with ASD and developmental delay (Van der Aa et al., 2012). De novo deletions involving the CMIP gene were identified in two additional patients diagnosed with ASD and ADHD and presenting with gastrointestinal issues in Luo et al., 2017. Polymorphisms in the CMIP gene have also been shown to associate with specific language impairment (Newbury et al., 2009), reading ability (Scerri et al., 2011), and language skills in ASD cohorts (Eicher and Gruen, 2015).

Krishnan Probability Score

Score 0.49164577814505

Ranking 5300/25841 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.
Original Source
ExAC Score

Score 0.99988658718418

Ranking 694/18225 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
Original Source
Sanders TADA Score

Score 0.94168726221243

Ranking 15025/18665 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).
Original Source
Zhang D Score

Score 0.25228849652439

Ranking 3455/20870 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.
Original Source
Interactome
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
P2RY1 purinergic receptor P2Y, G-protein coupled, 1 Human Protein Binding 5028 P47900
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