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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.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
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
DD
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
Support
ASD
DD, ID
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.

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 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 
  et al.  

Common

Variant ID
Polymorphism
SNP ID
Allele Change
Residue Change
Population Origin
Population Stage
Author, Year
 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 
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
17
Duplication
 2
 
17
Deletion-Duplication
 27
 
17
Deletion
 2
 
17
Deletion-Duplication
 74
 

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

Type
Title
Author, Year
Primary
A Conserved Circadian Function for the Neurofibromatosis 1 Gene.

F_NF1_1_KO_HM

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:

F_NF1_2_CKD_HM

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:

F_NF1_1_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Circadian rhythm: protein expression periodicity1
Decreased
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
Circadian rhythm1
Decreased
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
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
Description: Nf1 mutants showed a robust increase in calcium levels in SIFa-producing cells compared to controls.
 Calcium imaging
 Unreported
Gene expression1
Increased
Description: Nf1 mutant flies showed an increase in SIF1 mRNA expression compared to controls.
 Quantitative pcr (qrt-pcr)
 Unreported
Protein expression level evidence1
Decreased
Description: Nf1 mutant flies showed a decrease in SIFa protein expression compared to controls.
 Immunohistochemistry
 Unreported
Circadian rhythm1
 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

F_NF1_2_CKD_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Circadian rhythm1
Decreased
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


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

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