Human Gene Module / Chromosome 1 / MACF1

MACF1microtubule actin crosslinking factor 1

SFARI Gene Score
3S
Suggestive Evidence, Syndromic Criteria 3.1, Syndromic
Autism Reports / Total Reports
7 / 9
Rare Variants / Common Variants
20 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
1p34.3
Associated Disorders
-
Relevance to Autism

Multiple de novo variants in the MACF1 gene, including several missense variants, have been identified in ASD probands (Iossifov et al., 2014; Yuen et al., 2017; Satterstrom et al., 2020; Zhou et al., 2022), while inherited missense variants in this gene were identified in at least two diagnosed autistic individuals and absent in all non-autistic individuals in two separate multiplex ASD families in More et al., 2023. Heterozygous mutations in MACF1 are responsible for lissencephaly-9 with complex brainstem malformation (LIS9; OMIM 618325), an autosomal dominant neurologic disorder characterized by global developmental delay apparent since infancy, impaired intellectual development with poor or absent speech, and sometimes abnormal or involuntary movements associated with abnormal brain imaging that typically shows pachygyria, lissencephaly, and malformation of the brainstem consistent with a neuronal migration defect (Dobyns et al., 2018); two of the eight individuals with this disorder in this report presented with hand stereotypies. Macf1-mutant mice have been shown to exhibit social deficits and aberrant emotional behaviors (Ka et al., 2022).

Molecular Function

This gene encodes a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. The encoded protein is a member of a family of proteins that form bridges between different cytoskeletal elements. This protein facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Deletion of Macf1 in the mouse cerebral cortex during cortical development results in double cortex/subcortical band heterotopia and disrupted cortical lamination (Ka et al., 2022).

SFARI Genomic Platforms
Reports related to MACF1 (9 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
3 Support Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder Takata A , et al. (2018) Yes -
4 Support - Dobyns WB et al. (2018) No Stereotypy
5 Support Both rare and common genetic variants contribute to autism in the Faroe Islands Leblond CS , et al. (2019) Yes -
6 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
7 Support - Ka M et al. (2022) No Social deficits
8 Support - Zhou X et al. (2022) Yes -
9 Support - More RP et al. (2023) Yes -
Rare Variants   (20)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo - - 30471716 Dobyns WB et al. (2018)
c.4629+3858A>G - intron_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.7366A>G p.Lys2456Glu missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.4629+8163_4629+8164del - intron_variant De novo - - 35982159 Zhou X et al. (2022)
c.11308A>G p.Met3770Val missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.14116G>C p.Gly4706Arg missense_variant De novo - - 30471716 Dobyns WB et al. (2018)
c.15530G>T p.Cys5177Phe missense_variant De novo - - 30471716 Dobyns WB et al. (2018)
c.15682G>T p.Asp5228Tyr missense_variant De novo - - 30471716 Dobyns WB et al. (2018)
c.15688T>G p.Cys5230Gly missense_variant De novo - - 30471716 Dobyns WB et al. (2018)
c.427C>T p.Leu143= synonymous_variant De novo - Simplex 28263302 C Yuen RK et al. (2017)
c.10801C>T p.Arg3601Ter stop_gained Unknown - Simplex 30675382 Leblond CS , et al. (2019)
c.12480T>C p.Ile4160= synonymous_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.2444G>T p.Cys815Phe missense_variant Familial - Multiplex 36702863 More RP et al. (2023)
c.8941G>T p.Ala2981Ser missense_variant Familial - Multiplex 36702863 More RP et al. (2023)
c.6991A>G p.Met2331Val missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.11584_11585delinsAT p.Gln3862Ile missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.18004G>A p.Glu6002Lys missense_variant Unknown - Simplex 30675382 Leblond CS , et al. (2019)
c.4629+6036_4629+6037dup - intron_variant De novo - Simplex 31981491 Satterstrom FK et al. (2020)
c.14386del p.Gln4796SerfsTer10 frameshift_variant De novo - Simplex 29346770 Takata A , et al. (2018)
c.15689G>T p.Cys5230Phe missense_variant De novo - Multiplex (monozygotic twins) 30471716 Dobyns WB et al. (2018)
Common Variants  

No common variants reported.

SFARI Gene score
3S

Suggestive Evidence, Syndromic

Score Delta: Score remained at 3S

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."

4/1/2023
icon
3S

Increased from to 3S

Krishnan Probability Score

Score 0.50369154801148

Ranking 1938/25841 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 1

Ranking 2/18225 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
Iossifov Probability Score

Score 0.994

Ranking 20/239 scored genes


[Show Scoring Methodology]
Supplementary dataset S2 in the paper by Iossifov et al. (PNAS 112, E5600-E5607 (2015)) lists 239 genes with a probability of at least 0.8 of being associated with autism risk (column I). This probability metric combines the evidence from de novo likely-gene- disrupting and missense mutations and assesses it against the background mutation rate in unaffected individuals from the University of Washington’s Exome Variant Sequence database (evs.gs.washington.edu/EVS/). The list of probability scores can be found here: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1516376112/- /DCSupplemental/pnas.1516376112.sd02.xlsx
Sanders TADA Score

Score 0.95081226178184

Ranking 18638/18665 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 0.31081509766811

Ranking 2578/20870 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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