Summary Statistics:
ASD Reports: 39
Recent Reports: 11
Annotated variants: 48
Associated CNVs: 4
Evidence score: 5
Gene Score: S
Relevance to Autism
Neurofibromatosis is a Mendelian disease associated with autism. There is some association and linkage evidence implicating it in idiopathic autism, including positive association that was found with a NF1 polymorphism in the Japanese population (Marui et al., 2004). Chisholm et al., 2022 analyzed a study cohort of 68 children (3-15 years) with neurofibromatosis type I (NF1) who had scored above threshold on the Social Responsiveness Scale-Second Edition (T-score 60; 51% larger cohort) and completed the Autism Diagnostic Interview-Revised (ADI-R) and/or the Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) and found that 63% met the ADOS-2 'autism spectrum' cut-off, while 34% exceeded the more stringent threshold for 'autistic disorder' on the ADI-R. Large-scale whole-exome and whole-genome seqeuncing studies have identified de novo variants in ASD probands from the Simons Simplex Collection, the Autism Sequencing Consortium, the MSSNG cohort, and the SPARK cohort (Sanders et al., 2012; Iossifov et al., 2014; Zhou et al., 2022). A two-stage analysis of rare de novo and inherited coding variants in 42,607 ASD cases, including 35,130 new cases from the SPARK cohort, in Zhou et al., 2022 identified NF1 as a gene reaching exome-wide significance (P < 2.5E-06).
Molecular Function
The encoded protein has Ras GTPase activity and appears to be a negative regulator of cell proliferation.
References
Primary
Association between the neurofibromatosis-1 (NF1) locus and autism in the Japanese population.
ASD
Negative Association
Lack of association of the (AAAT)6 allele of the GXAlu tetranucleotide repeat in intron 27b of the NF1 gene with autism.
ASD
Negative Association
Association study of the NF1 gene and autistic disorder.
ASD
Support
High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.
Epilepsy/seizures
DD/ID
Support
Genetic care in geographically isolated small island communities: 8 years of experience in the Dutch Caribbean
DD
Support
Neurofibromatosis type I, ASD
Support
Clinical exome sequencing: results from 2819 samples reflecting 1000 families.
Hypotonia
ASD
Support
Behavioural and psychological features of PTEN mutations: a systematic review of the literature and meta-analysis of the prevalence of autism spectrum disorder characteristics
Neurofibromatosis type I
ASD
Support
ASD
ID, learning disability
Support
Large-scale discovery of novel genetic causes of developmental disorders.
Palsy, motor neuron atrophy, muscle weakness
Support
A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies
ASD
Support
Loss of NF1 in Drosophila Larvae Causes Tactile Hypersensitivity and Impaired Synaptic Transmission at the Neuromuscular Junction
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Neurofibromatosis type I
Support
A novel RAB39B mutation and concurrent de novo NF1 mutation in a boy with neurofibromatosis type 1, intellectual disability, and autism: a case report
Neurofibromatosis type 1
ASD, ID, epilepsy/seizures
Support
Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder
ASD
Neurofibromatosis type I
Support
Exome sequencing in multiplex autism families suggests a major role for heterozygous truncating mutations.
ASD
Support
Targeted resequencing of 358 candidate genes for autism spectrum disorder in a Chinese cohort reveals diagnostic potential and genotype-phenotype c...
ASD
Support
Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China
ASD
Support
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
ASD
Support
Early-onset epileptic encephalopathy and severe developmental delay in an association with de novo double mutations in NF1 and MAGEL2.
Neurofibromatosis type 1
DD, epilepsy/seizures
Support
Genetic and Phenotype Analysis of a Chinese Cohort of Infants and Children With Epilepsy
Epilepsy/seizures
Support
De novo mutations revealed by whole-exome sequencing are strongly associated with autism.
ASD
Highly Cited
The NF1 locus encodes a protein functionally related to mammalian GAP and yeast IRA proteins.
Highly Cited
Mechanism for the learning deficits in a mouse model of neurofibromatosis type 1.
Recent Recommendation
Neurofibromin is a novel regulator of RAS-induced signals in primary vascular smooth muscle cells.
Recent Recommendation
Autism traits in the RASopathies.
Neurofibromatosis type 1
Autistic features
Recent Recommendation
Autism and other psychiatric comorbidity in neurofibromatosis type 1: evidence from a population-based study.
Recent Recommendation
ERK inhibition rescues defects in fate specification of Nf1-deficient neural progenitors and brain abnormalities.
Recent Recommendation
Integrating de novo and inherited variants in 42
ASD
Recent Recommendation
Behavioural and cognitive phenotypes in children with neurofibromatosis type 1 (NF1): the link with the neurobiological level.
Recent Recommendation
Cerebral volumetric abnormalities in Neurofibromatosis type 1: associations with parent ratings of social and attention problems, executive dysfunc...
Recent Recommendation
Aberrant expression of synaptic plasticity-related genes in the NF1 mouse hippocampus.
Recent Recommendation
Prevalence of Autism Spectrum Disorder symptoms in children with neurofibromatosis type 1.
Recent Recommendation
Neurofibromin regulation of ERK signaling modulates GABA release and learning.
Recent Recommendation
Neurofibromatosis type 1 and autism spectrum disorder.
GEN169R001
microsatellite
GEN169R002
missense_variant
c.7375C>A
p.His2459Asn
De novo
Simplex
GEN169R003
copy_number_loss
Familial
Maternal
Unknown
GEN169R004
missense_variant
c.7910G>A
p.Arg2637Gln
Familial
Paternal
Multiplex
GEN169R005
missense_variant
c.5425C>T
p.Pro1809Ser
De novo
Simplex
GEN169R006
stop_gained
c.3449C>G
p.Ser1150Ter
De novo
Simplex
GEN169R007
missense_variant
c.107C>G
p.Thr36Ser
Familial
Maternal
GEN169R008
stop_gained
c.5327C>A
p.Ser1776Ter
De novo
Simplex
GEN169R009
stop_gained
c.6792C>G
p.Tyr2264Ter
De novo
Simplex
GEN169R010
splice_site_variant
c.4772+1G>T
De novo
GEN169R011
frameshift_variant
c.1742dup
p.Cys582LeufsTer6
Familial
Maternal
GEN169R012
frameshift_variant
c.1742dup
p.Cys582LeufsTer6
Familial
Maternal
GEN169R013
frameshift_variant
c.1742dup
p.Cys582LeufsTer6
Familial
Maternal
GEN169R014
splice_site_variant
c.6579+2T>C
De novo
Extended multiplex
GEN169R015
splice_site_variant
c.888+2T>G
De novo
Simplex
GEN169R016
missense_variant
c.4267A>G
p.Lys1423Glu
Unknown
GEN169R017
missense_variant
c.1885G>A
p.Gly629Arg
De novo
GEN169R018
frameshift_variant
c.701del
p.Leu234ArgfsTer47
Unknown
GEN169R019
splice_site_variant
c.731-1G>T
Unknown
GEN169R020
missense_variant
c.5794C>G
p.Leu1932Val
De novo
GEN169R021
stop_gained
c.6930T>A
p.Pro2310%3D
De novo
GEN169R022
splice_site_variant
c.7000-1G>C
De novo
GEN169R023
synonymous_variant
c.4143C>T
p.Ile1381%3D
De novo
Multiplex
GEN169R024
splice_site_variant
c.4772+2T>C
De novo
Simplex
GEN169R025
frameshift_variant
c.5754del
p.Asn1918LysfsTer7
De novo
Simplex
GEN169R026
frameshift_variant
c.653_654delinsT
p.Lys218MetfsTer7
De novo
GEN169R027
missense_variant
c.2684T>G
p.Met895Arg
De novo
GEN169R028
frameshift_variant
c.3938_3941del
p.Asp1313GlyfsTer13
De novo
GEN169R029
stop_gained
c.6792C>A
p.Tyr2264Ter
De novo
GEN169R030
synonymous_variant
c.7470C>T
p.Val2490%3D
De novo
GEN169R031
frameshift_variant
c.7622_7623del
p.Gly2541AspfsTer14
De novo
GEN169R032
missense_variant
c.8164C>G
p.Leu2722Val
De novo
GEN169R033
stop_gained
c.1246C>T
p.Arg416Ter
De novo
GEN169R034
splice_site_variant
c.3496+2T>G
De novo
GEN169R035
splice_site_variant
c.4207G>T
p.Ala1403Ser
De novo
GEN169R036
missense_variant
c.4562T>G
p.Leu1521Arg
De novo
GEN169R037
missense_variant
c.7163C>T
p.Thr2388Ile
De novo
GEN169R038
stop_gained
c.7846C>T
p.Gln2616Ter
De novo
GEN169R039
missense_variant
c.3089C>T
p.Ser1030Leu
Familial
Paternal
GEN169R040
frameshift_variant
c.7996_7997del
p.Asn2666HisfsTer26
Familial
Maternal
GEN169R041
splice_site_variant
c.6938del
p.Gly2313ValfsTer12
Familial
Maternal
GEN169R042
frameshift_variant
c.499_502del
p.Cys167GlnfsTer10
Familial
Paternal
Simplex
GEN169R043
splice_site_variant
c.7395-2A>T
p.?
De novo
GEN169R044
stop_gained
c.2041C>T
p.Arg681Ter
De novo
Simplex
GEN169R045
missense_variant
c.8188C>T
p.Leu2730Phe
Unknown
Simplex
GEN169R046
splice_site_variant
c.3113+1G>A
Familial
Paternal
Multiplex
GEN169C001
microsatellite, intron_variant
N/A
N/A
Japanese ASD cases (n = 74) and controls (n = 122)
Discovery
GEN169C002
microsatellite, intron_variant
N/A
N/A
Japanese ASD cases (n = 74) and controls (n = 122)
Discovery
17
Deletion-Duplication
27
17
Deletion-Duplication
74
Summary Statistics:
# of Reports: 1
# of Models: 21
External Links
Model Summary
Nf1 mutant flies showed reduced rhythmicty in rest:activity patterns as well as some changes in gene and protein expression. The rhythmicity patterns were rescued by conditional expression in different neuronal populations.
References
Primary
A Conserved Circadian Function for the Neurofibromatosis 1 Gene.
Model Type:
Genetic
Model Genotype:
Homozygous
Mutation:
A null mutation in the Nf1 gene was generated either by deletion (Nf1^P1) or by P-element insertion (Nf1^P2) (Williams et al., 2001). These flies are Nf1P1/P2.
Allele Type: Loss-of-function
Strain of Origin:
Genetic Background:
ES Cell Line:
Mutant ES Cell Line:
Model Source:
Model Type:
Genetic
Model Genotype:
Homozygous
Mutation:
RNAi-mediated knockdown of Nf1 with an inducible pan-neuronal driver (Nsyb-GS). Knocked down expression was driven specifically in adults by feeding flies RU-486.
Allele Type: Loss-of-function
Strain of Origin:
Genetic Background:
ES Cell Line:
Mutant ES Cell Line:
Model Source:
Circadian rhythm: protein expression periodicity1
Decreased
View More
Description: Nf1 mutant flies showed a decrease in PDF protein expression compared to controls.
Exp Paradigm: Protein expression measured at two time points (CT1 and CT13) in flies maintained in constant darkness (DD).
Immunohistochemistry
Unreported
Decreased
View More
Description: Nf1 mutant flies showed a dramatic decrease in rhythmicity (8.9% of flies were rhythmic) compared to controls.
General observations
Unreported
Ion influx and permeability: calcium1
Abnormal
View More
Description: Nf1 mutants showed do not show change or cycling in overall calcium levels compared to controls in light:dark cycles, that is observed in DH44 cells
Exp Paradigm: Calcium levels were measured at ZT1 and ZT13.
Calcium imaging
Unreported
Ion influx and permeability: calcium1
Increased
View More
Description: Nf1 mutants showed a robust increase in calcium levels in SIFa-producing cells compared to controls.
Calcium imaging
Unreported
Increased
View More
Description: Nf1 mutant flies showed an increase in SIF1 mRNA expression compared to controls.
Quantitative pcr (qrt-pcr)
Unreported
Protein expression level evidence1
Decreased
View More
Description: Nf1 mutant flies showed a decrease in SIFa protein expression compared to controls.
Immunohistochemistry
Unreported
No change
Calcium imaging
Unreported
Circadian rhythm: protein expression periodicity1
No change
Immunohistochemistry
Unreported
Protein expression level evidence1
No change
Immunohistochemistry
Unreported
Not Reported:
Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Physiological parameters, Repetitive behavior, Seizure, Sensory, Social behavior
Decreased
View More
Description: Nf1 mutants showed reduced strength of circadian rhythms compared to controls.
General observations
Adult
Not Reported:
Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure, Sensory, Social behavior
Summary Statistics:
Total Interactions: 40
Total Publications: 19
Show all nodes
Hide non-ASD
Interactor Symbol
Interactor Name
Interactor Organism
Entrez ID
Uniprot ID
Interaction Type
Evidence
Reference
APP
amyloid beta (A4) precursor protein
351
P05067
Y2H; IP/WB
De Schepper S , et al. 2005
C19ORF75
SIGLEC family-like protein 1
284369
Q8N7X8
IP; LC-MS/MS
Huttlin EL , et al. 2015
CA14
Carbonic anhydrase 14
23632
Q9ULX7
IP; LC-MS/MS
Huttlin EL , et al. 2015
CD79B
B-cell antigen receptor complex-associated protein beta chain
974
P40259-2
IP; LC-MS/MS
Huttlin EL , et al. 2015
DNAJC7
DnaJ (Hsp40) homolog, subfamily C, member 7
7266
Q99615
Y2H
Murthy AE , et al. 1996
EFS
embryonal Fyn-associated substrate
10278
O43281
Y2H
Sakai Y , et al. 2011
EPHA1
EPH receptor A1
2041
P21709
IP; LC-MS/MS
Huttlin EL , et al. 2015
FAM174A
Membrane protein FAM174A
345757
Q8TBP5
IP; LC-MS/MS
Huttlin EL , et al. 2015
HRAS
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
3265
P01112
IP/WB
Hirata Y , et al. 2015
HRAS
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
3265
P01112
Y2H; GTP hydrolysis assay
Morcos P , et al. 1996
P4HA3
prolyl 4-hydroxylase, alpha polypeptide III
283208
Q7Z4N8
IP; LC-MS/MS
Huttlin EL , et al. 2015
SCN3B
sodium channel, voltage-gated, type III, beta subunit
55800
Q9NY72
IP; LC-MS/MS
Huttlin EL , et al. 2015
SDC1
syndecan 1
6382
P18827
Y2H
Hsueh YP , et al. 2001
SDC2
syndecan 2
6383
P34741
Y2H; GST
Hsueh YP , et al. 2001
SDC3
syndecan 3
9672
O75056
Y2H; IP/WB
Hsueh YP , et al. 2001
SDC4
syndecan 4
6385
P31431
Y2H
Hsueh YP , et al. 2001
SPRED1
Sprouty-related, EVH1 domain-containing protein 1
161742
Q7Z699
IP/WB
Pasmant E , et al. 2014
SPRED1
Sprouty-related, EVH1 domain-containing protein 1
161742
Q7Z699
Y2H; IP/WB
Hirata Y , et al. 2015
TBPL1
TBP-like 1
9519
P62380
PIP
Chong JA , et al. 2005
TNFSF13B
Tumor necrosis factor ligand superfamily member 13B
10673
Q9Y275
IP; LC-MS/MS
Huttlin EL , et al. 2015
TOP3B
topoisomerase (DNA) III beta
8940
O95985
HITS-CLIP
Xu D , et al. 2013
TTC1
tetratricopeptide repeat domain 1
7265
Q99614
Y2H
Murthy AE , et al. 1996
VSIG1
V-set and immunoglobulin domain-containing protein 1
340547
Q86XK7
IP; LC-MS/MS
Huttlin EL , et al. 2015
Actg1
actin, gamma, cytoplasmic 1
11465
P63260
IP; LC-MS/MS
Omrani A , et al. 2015
Cul3
cullin 3
26554
Q9JLV5
IP/WB
Hollstein PE and Cichowski K 2013
Dpysl2
dihydropyrimidinase-like 2
12934
O08553
IP; LC-MS/MS
Omrani A , et al. 2015
FMR1
fragile X mental retardation 1
14265
P35922
HITS-CLIP
Darnell JC , et al. 2011
Grin1
glutamate receptor, ionotropic, NMDA1 (zeta 1)
14810
P35438
Affinity chromatography; IP/WB
Husi H , et al. 2000
Grin2b
glutamate receptor, ionotropic, NMDA2B (epsilon 2)
14812
Q01097
Peptide affinity chromatography
Husi H , et al. 2000
Hcn1
hyperpolarization-activated, cyclic nucleotide-gated K+ 1
15165
O88704
IP; LC-MS/MS; IP/WB
Omrani A , et al. 2015
Mbp
myelin basic protein
17196
P04370
IP; LC-MS/MS
Omrani A , et al. 2015
MET
met proto-oncogene
17295
P16056
IP; LC-MS/MS
Xie Z , et al. 2016
Paics
phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase
67054
Q9DCL9
IP; LC-MS/MS
Omrani A , et al. 2015
Tuba1a
tubulin, alpha 1A
22142
P68369
IP; LC-MS/MS
Omrani A , et al. 2015
Tubb4a
tubulin, beta 4A class IVA
22153
Q9D6F9
IP; LC-MS/MS
Omrani A , et al. 2015
Cask
calcium/calmodulin-dependent serine protein kinase (MAGUK family)
29647
Q62915
IP/WB
Hsueh YP , et al. 2001
Ddah1
dimethylarginine dimethylaminohydrolase 1
64157
O08557
GST; Reversed-phase chromatography (RPC)
Tokuo H , et al. 2001
MIB1
mindbomb E3 ubiquitin protein ligase 1
307594
D3ZUV2
Affinity chromatography; LC-MS/MS
Mertz J , et al. 2015
miR16
microRNA mir-16
100313997
N/A
Peptide microarray; in silico target prediction
Pan Q , et al. 2014
EHMT1
G9a
30971
Q95RU8
ChIP-Seq
Kramer JM , et al. 2011