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Relevance to Autism

Biallelic variants in the KPTN gene were found to cosegregate with the disease phenotype in nine family members from four nuclear families from the Amish community of Ohio presenting with an inherited variable form of neurodevelopmental delay (most consistent features were global developmental delay, macrocephaly with frontal bossing, high levels of anxiety, and some features suggestive of pervasive developmental disorder, such as stereotypies and/or repetitive speech) in Baple et al., 2013. A homozygous frameshift variant in the KPTN gene was identified in two adult siblings from Estonia presenting with moderate intellectual disability and macrocephaly in Pajusalu et al., 2015; the male sibling also presented with behavioral problems, including autistic features.

Molecular Function

This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.
DD, ID
Epilepsy/seizures, autistic features
Support
Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism.
ASD
Support
Novel homozygous mutation in KPTN gene causing a familial intellectual disability-macrocephaly syndrome.
ID, macrocephaly
Epilepsy/seizures, autistic features
Support
Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability
Autosomal recessive mental retardation-41
Support
Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing
Autosomal recessive mental retardation-41
ASD
Support
Clinical genome sequencing in an unbiased pediatric cohort.
Autosomal recessive mental retardation-41 (MRT41)
ASD, ID, epilepsy/seizures, macrocephaly

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN586R001a 
 stop_gained 
 c.776C>A 
 p.Ser259Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN586R002a 
 stop_gained 
 c.608C>A 
 p.Ser203Ter 
 Familial 
 Both parents 
 Simplex 
 GEN586R003a 
 inframe_insertion 
 c.546_547insTCTGCAGATGTGGTCGGT 
 p.Val182_Leu183insSerAlaAspValValGly 
 Familial 
 Paternal 
 Multiplex 
 GEN586R003b 
 stop_gained 
 c.776C>A 
 p.Ser259Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN586R004a 
 inframe_insertion 
 c.546_547insTCTGCAGATGTGGTCGGT 
 p.Val182_Leu183insSerAlaAspValValGly 
 Familial 
 Paternal 
 Multiplex 
 GEN586R004b 
 stop_gained 
 c.776C>A 
 p.Ser259Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN586R005a 
 frameshift_variant 
 c.497dup 
 p.Ser167GlufsTer50 
 Familial 
 Both parents 
 Multiplex 
 GEN586R006 
 synonymous_variant 
 c.279G>T 
 p.Arg93= 
 De novo 
 NA 
 Simplex 
 GEN586R007a 
 inframe_insertion 
 c.546_547insTCTGCAGATGTGGTCGGT 
 p.Val182_Leu183insSerAlaAspValValGly 
 Unknown 
  
  
 GEN586R007b 
 splice_site_variant 
 c.227-79G>A 
  
 Unknown 
  
  
 GEN586R008a 
 splice_site_variant 
 c.227-79G>A 
  
 Familial 
 Maternal 
 Simplex 
 GEN586R008b 
 inframe_insertion 
 c.546_547insTCTGCAGATGTGGTCGGT 
 p.Val182_Leu183insSerAlaAspValValGly 
 Familial 
 Paternal 
 Simplex 
 GEN586R009a 
 frameshift_variant 
 c.429_430insTA 
 p.Ser144Ter 
 Familial 
 Both parents 
 Multiplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
19
Deletion-Duplication
 13
 
19
Duplication
 2
 

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
AMD1 adenosylmethionine decarboxylase 1 262 P17707 IP; LC-MS/MS
Huttlin EL , et al. 2015
BTN2A1 butyrophilin, subfamily 2, member A1 11120 Q7KYR7 IP; LC-MS/MS
Huttlin EL , et al. 2015
C10ORF47 proline and serine-rich protein 2 254427 Q86WR7 IP; LC-MS/MS
Huttlin EL , et al. 2015
C12ORF66 chromosome 12 open reading frame 66 144577 Q96MD2 IP; LC-MS/MS
Huttlin EL , et al. 2015
C7ORF60 chromosome 7 open reading frame 60 154743 Q1RMZ1 IP; LC-MS/MS
Huttlin EL , et al. 2015
CHD8 chromodomain helicase DNA binding protein 8 57680 Q9HCK8 CHIP-seq
Cotney J , et al. 2015
DPH1 DPH1 homolog (S. cerevisiae) 1801 B3KQW7 IP; LC-MS/MS
Huttlin EL , et al. 2015
ELP2 elongator acetyltransferase complex subunit 2 55250 Q6IA86 IP; LC-MS/MS
Huttlin EL , et al. 2015
ELP3 elongator acetyltransferase complex subunit 3 55140 Q9H9T3 IP; LC-MS/MS
Huttlin EL , et al. 2015
FMN2 formin 2 56776 Q9HBL1 IP; LC-MS/MS
Huttlin EL , et al. 2015
GTSE1 G-2 and S-phase expressed 1 51512 Q9NYZ3 IP; LC-MS/MS
Huttlin EL , et al. 2015
HSPB9 Heat shock protein beta-9 94086 Q9BQS6 IP; LC-MS/MS
Huttlin EL , et al. 2015
ITFG2 Integrin-alpha FG-GAP repeat-containing protein 2 55846 Q969R8 IP; LC-MS/MS
Huttlin EL , et al. 2015
KIAA0467 seizure threshold 2 homolog (mouse) 23334 Q5T011 IP; LC-MS/MS
Huttlin EL , et al. 2015
KIF5B kinesin family member 5B 3799 P33176 IP; LC-MS/MS
Huttlin EL , et al. 2015
KLC1 kinesin light chain 1 3831 Q07866 IP; LC-MS/MS
Huttlin EL , et al. 2015
KLC2 kinesin light chain 2 64837 Q9H0B6 IP; LC-MS/MS
Huttlin EL , et al. 2015
KLC4 kinesin light chain 4 89953 Q9NSK0 IP; LC-MS/MS
Huttlin EL , et al. 2015
KLHL15 kelch-like family member 15 80311 Q96M94 IP; LC-MS/MS
Huttlin EL , et al. 2015
MAVS mitochondrial antiviral signaling protein 57506 Q7Z434 IP; LC-MS/MS
Huttlin EL , et al. 2015
NFRKB nuclear factor related to kappaB binding protein 4798 Q6P4R8 IP; LC-MS/MS
Huttlin EL , et al. 2015
RBM33 RNA binding motif protein 33 155435 Q96EV2 IP; LC-MS/MS
Huttlin EL , et al. 2015
RNASEH2A ribonuclease H2, subunit A 10535 O75792 IP; LC-MS/MS
Huttlin EL , et al. 2015
TES testis derived transcript (3 LIM domains) 26136 A4D0U5 IP; LC-MS/MS
Huttlin EL , et al. 2015
TMCO4 Transmembrane and coiled-coil domain-containing protein 4 255104 Q5TGY1 IP; LC-MS/MS
Huttlin EL , et al. 2015
TSPAN7 tetraspanin 7 7102 P41732 LC/ESI/MS/MS
Ewing RM , et al. 2007
VWCE von Willebrand factor C and EGF domain-containing protein 220001 Q96DN2 IP; LC-MS/MS
Huttlin EL , et al. 2015

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