Human Gene Module / Chromosome 10 / MKX

MKXmohawk homeobox

SFARI Gene Score
High Confidence Criteria 1.1
Autism Reports / Total Reports
2 / 3
Rare Variants / Common Variants
4 / 0
Limited Learn More
MKX, C10orf48,  IFRX,  IRXL1
Associated Syndromes
Chromosome Band
Associated Disorders
Genetic Category
Rare Single Gene Mutation
Relevance to Autism

Two de novo missense variants that were predicted to be probably damaging (defined as MPC 2) were identified in the MKX gene in ASD probands from the Autism Sequencing Consoritum, while an additional protein-truncating variant in this gene was observed in a case sample from the Danish iPSYCH study (Satterstrom et al., 2020). TADA analysis of de novo variants from the Simons Simplex Collection and the Autism Sequencing Consortium and protein-truncating variants from iPSYCH in Satterstrom et al., 2020 identified MKX as a candidate gene with a false discovery rate (FDR) 0.01.

Molecular Function

The protein encoded by this gene is an IRX family-related homeobox protein that may play a role in cell adhesion.

SFARI Genomic Platforms
Reports related to MKX (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
2 Support - Yap CX et al. (2021) Yes -
3 Support - N.Y.) (07/2) No -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Familial Maternal - 33568206 Yap CX et al. (2021)
c.794C>A p.Ser265Tyr missense_variant De novo NA - 35901164 N.Y.) (07/2)
c.265C>T p.Leu89Phe missense_variant De novo NA Simplex 31981491 Satterstrom FK et al. (2020)
c.277C>G p.Arg93Gly missense_variant De novo NA Multiplex 31981491 Satterstrom FK et al. (2020)
Common Variants  

No common variants reported.

SFARI Gene score

High Confidence

Score Delta: Score remained at 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.


Increased from to 1

Krishnan Probability Score

Score 0.50387929358909

Ranking 1935/25841 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: A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at
ExAC Score

Score 0.88232008640152

Ranking 3360/18225 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 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: aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.92838679680356

Ranking 10902/18665 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
Zhang D Score

Score -0.1346488397686

Ranking 13645/20870 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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