Summary Statistics:
ASD Reports: 14
Recent Reports: 1
Annotated variants: 94
Associated CNVs: 4
Evidence score: 3
Gene Score:
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).
References
Primary
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Identification of MACF1 as a causative gene of generalised epilepsy
Epilepsy/seizures
ASD, DD, ID
Support
Both rare and common genetic variants contribute to autism in the Faroe Islands.
ASD
Support
Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort
ASD, DD
Support
Lissencephaly-9 with complex brainstem malformatio
Stereotypy
Support
Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism
ASD
Support
Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder.
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Lissencephaly-9 with complex brainstem malformatio
Social deficits
Support
Deleterious coding variation associated with autism is shared across ancestries.
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Recent Recommendation
A clinical and genotype-phenotype analysis of MACF1 variants
Lissencephaly 9 with complex brainstem malformatio
ASD
GEN1390R001
missense_variant
c.6991A>G
p.Met2331Val
De novo
Simplex
GEN1390R002
synonymous_variant
c.427C>T
p.Leu143=
De novo
Simplex
GEN1390R003
missense_variant
c.18004G>A
p.Glu6002Lys
Unknown
Simplex
GEN1390R004
stop_gained
c.10801C>T
p.Arg3601Ter
Unknown
Simplex
GEN1390R005
synonymous_variant
c.12480T>C
p.Ile4160=
De novo
GEN1390R006
intron_variant
c.4629+6036_4629+6037dup
De novo
Simplex
GEN1390R007
intron_variant
c.4629+3858A>G
De novo
GEN1390R008
intron_variant
c.4629+8163_4629+8164del
De novo
GEN1390R009
missense_variant
c.7366A>G
p.Lys2456Glu
De novo
GEN1390R010
missense_variant
c.11308A>G
p.Met3770Val
De novo
GEN1390R011
missense_variant
c.11584_11585delinsAT
p.Gln3862Ile
De novo
GEN1390R012
missense_variant
c.8941G>T
p.Ala2981Ser
Familial
Multiplex
GEN1390R013
missense_variant
c.2444G>T
p.Cys815Phe
Familial
Multiplex
GEN1390R014
missense_variant
c.15530G>T
p.Cys5177Phe
De novo
GEN1390R015
missense_variant
c.15530G>T
p.Cys5177Phe
De novo
GEN1390R016
missense_variant
c.15682G>T
p.Asp5228Tyr
De novo
GEN1390R017
missense_variant
c.15682G>T
p.Asp5228Tyr
De novo
GEN1390R018
missense_variant
c.15689G>T
p.Cys5230Phe
De novo
Multiplex (monozygotic twins)
GEN1390R019
missense_variant
c.15688T>G
p.Cys5230Gly
De novo
GEN1390R020
copy_number_loss
De novo
GEN1390R021
missense_variant
c.14116G>C
p.Gly4706Arg
De novo
GEN1390R022
frameshift_variant
c.14386del
p.Gln4796SerfsTer10
De novo
Simplex
GEN1390R023
missense_variant
c.2342C>T
p.Thr781Ile
De novo
GEN1390R024
missense_variant
c.16462A>C
p.Ile5488Leu
De novo
GEN1390R025
missense_variant
c.17495T>C
p.Met5832Thr
De novo
GEN1390R026
missense_variant
c.3005A>C
p.Gln1002Pro
Unknown
GEN1390R027
missense_variant
c.9905A>G
p.Asn3302Ser
De novo
Simplex
GEN1390R028
missense_variant
c.14740C>T
p.Arg4914Cys
De novo
Simplex
GEN1390R029a
missense_variant
c.1556T>C
p.Leu519Ser
Familial
Paternal
Simplex
GEN1390R029b
missense_variant
c.11118T>A
p.Asp3706Glu
Familial
Maternal
Simplex
GEN1390R030a
missense_variant
c.3014G>A
p.Arg1005His
Familial
Paternal
Simplex
GEN1390R030b
missense_variant
c.7160A>G
p.His2387Arg
Familial
Maternal
Simplex
GEN1390R031a
missense_variant
c.3698G>A
p.Arg1233His
Familial
Paternal
Simplex
GEN1390R031b
missense_variant
c.2908G>T
p.Val970Leu
Familial
Maternal
Simplex
GEN1390R032a
missense_variant
c.5503G>A
p.Glu1835Lys
Familial
Paternal
Simplex
GEN1390R032b
missense_variant
c.8498A>T
p.Gln2833Leu
Familial
Maternal
Simplex
GEN1390R033a
missense_variant
c.6592A>T
p.Asn2198Tyr
Familial
Paternal
Simplex
GEN1390R033b
missense_variant
c.6245A>G
p.Gln2082Arg
Familial
Maternal
Simplex
GEN1390R034a
missense_variant
c.9617T>C
p.Leu3206Ser
Familial
Paternal
Simplex
GEN1390R034b
missense_variant
c.9292G>A
p.Glu3098Lys
Familial
Maternal
Simplex
GEN1390R035a
missense_variant
c.14785C>A
p.Leu4929Met
Familial
Paternal
Simplex
GEN1390R035b
missense_variant
c.6245A>G
p.Gln2082Arg
Familial
Maternal
Simplex
GEN1390R036a
missense_variant
c.16180G>A
p.Ala5394Thr
Familial
Paternal
Simplex
GEN1390R036b
missense_variant
c.12404C>T
p.Ala4135Val
Familial
Maternal
Simplex
GEN1390R037
missense_variant
c.21389G>A
p.Cys7130Tyr
De novo
GEN1390R038
missense_variant
c.21389G>C
p.Cys7130Ser
De novo
GEN1390R039
missense_variant
c.21394T>C
p.Cys7132Arg
Unknown
GEN1390R040
missense_variant
c.21394T>C
p.Cys7132Arg
De novo
GEN1390R041
missense_variant
c.21547G>T
p.Asp7183Tyr
Unknown
GEN1390R042
missense_variant
c.21553T>C
p.Cys7185Arg
Unknown
GEN1390R043
missense_variant
c.21440G>C
p.Arg7147Pro
De novo
GEN1390R044
missense_variant
c.21131T>C
p.Met7044Thr
De novo
GEN1390R045
missense_variant
c.21284A>G
p.Asp7095Gly
De novo
GEN1390R046a
stop_gained
c.70C>T
p.Arg24Ter
Familial
Both parents
GEN1390R047a
missense_variant
c.916G>A
p.Gly306Arg
Familial
GEN1390R047b
missense_variant
c.2033A>G
p.His678Arg
Familial
GEN1390R048a
missense_variant
c.2870T>G
p.Leu957Arg
Familial
GEN1390R048b
missense_variant
c.19393G>A
p.Ala6465Thr
Familial
GEN1390R049a
missense_variant
c.2885A>G
p.Tyr962Cys
Familial
Both parents
Multiplex
GEN1390R050a
missense_variant
c.3065T>G
p.Val1022Gly
Familial
Both parents
GEN1390R051a
inframe_deletion
c.3551_3553del
p.Glu1184del
Familial
GEN1390R051b
missense_variant
c.16879C>T
p.Arg5627Cys
Familial
GEN1390R052a
missense_variant
c.4060C>A
p.Leu1354Met
Familial
Both parents
GEN1390R053a
missense_variant
c.12782T>C
p.Ile4261Thr
Familial
Both parents
GEN1390R054a
missense_variant
c.18624T>G
p.Ile6208Met
Familial
Both parents
GEN1390R055a
missense_variant
c.1931G>T
p.Gly644Val
Familial
GEN1390R055b
missense_variant
c.20772G>A
p.Met6924Ile
Familial
GEN1390R056
missense_variant
c.2566G>A
p.Val856Ile
Familial
Maternal
GEN1390R057
missense_variant
c.4118G>A
p.Arg1373His
Unknown
GEN1390R058
splice_site_variant
c.10831-1G>A
p.?
Familial
Paternal
GEN1390R059a
missense_variant
c.11042A>C
p.Glu3681Ala
Familial
GEN1390R059b
missense_variant
c.14276A>C
p.Ile4759Thr
Familial
GEN1390R060
missense_variant
c.14957G>A
p.Arg4986Gln
Familial
Maternal
GEN1390R061a
missense_variant
c.15188T>A
p.Val5063Glu
Familial
GEN1390R061b
missense_variant
c.16481T>G
p.Ile5494Ser
Familial
GEN1390R062
intron_variant
G>A
Familial
Maternal
GEN1390R063
missense_variant
c.16613G>A
p.Gly5538Asp
Familial
Maternal
GEN1390R064
missense_variant
c.17630G>A
p.Arg5877His
Familial
GEN1390R065
stop_gained
c.20314C>T
p.Arg6772Ter
Familial
Paternal
GEN1390R066
missense_variant
c.112C>A
p.Pro38Thr
Unknown
Multiplex
GEN1390R067
intron_variant
c.543+11432C>T
p.?
De novo
GEN1390R068
missense_variant
c.2069C>T
p.Thr690Ile
De novo
GEN1390R069
missense_variant
c.3958A>G
p.Thr1320Ala
De novo
GEN1390R070
missense_variant
c.13795A>C
p.Met4599Leu
De novo
GEN1390R071
frameshift_variant
c.1163del
p.Gly388AlafsTer23
Unknown
GEN1390R072
splice_site_variant
c.3961-2A>G
p.?
De novo
Simplex
GEN1390R073
frameshift_variant
c.4418del
p.Glu1473GlyfsTer2
De novo
GEN1390R074
frameshift_variant
c.15192_ 15207del
p.Gln5065ArgfsTer2
Unknown
Multiplex
GEN1390R075
stop_gained
c.18994C>T
p.Gln6332Ter
De novo
GEN1390R076
copy_number_loss
De novo
GEN1390R077
copy_number_loss
De novo
GEN1390R078
copy_number_loss
De novo
GEN1390R079
missense_variant
c.7588G>A
p.Glu2530Lys
De novo
GEN1390R080
missense_variant
c.226C>T
p.Arg76Trp
De novo
No Common Variants Available
1
Deletion-Duplication
11
No Animal Model Data Available
No Interactions Available