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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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KPTN
kaptin, actin binding protein
Chromosome 19 Β· 19q13.32
NCBI Gene: 11133Ensembl: ENSG00000118162.15HGNC: HGNC:6404UniProt: A0A384NLB4
28PubMed Papers
21Diseases
0Drugs
22Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
filamentous actincellular response to amino acid starvationcellular response to glucose starvationprotein localization to lysosomemacrocephaly-developmental delay syndromegenetic disordercomplex neurodevelopmental disorderbrain aneurysm
✦AI Summary

KPTN encodes a protein that functions as a critical component of the KICSTOR complex, which negatively regulates mTORC1 signaling in response to nutrient availability 1. The KICSTOR complex, comprising KPTN, ITFG2, C12orf66, and SZT2, localizes to lysosomes and recruits the GATOR1 complex to the lysosomal surface, enabling proper amino acid-dependent mTORC1 regulation 12. Mechanistically, SZT2 forms a crescent-shaped scaffold that binds the ITFG2-KPTN heterodimer, and this complex positions GATOR1 on lysosomes through NPRL3 interactions 2. KPTN function is regulated by FBXO2-mediated ubiquitination, which disrupts KICSTOR assembly and impairs GATOR1 recruitment 3. Loss-of-function mutations in KPTN cause autosomal recessive intellectual developmental disorder 41 (MRT41), characterized by intellectual disability, macrocephaly, behavioral abnormalities, and epilepsy 456. The disorder results from hyperactive mTORC1 signaling due to failed nutrient sensing, leading to abnormal postnatal brain development and cognitive deficits 4. Mouse models demonstrate that KPTN deficiency causes brain overgrowth and cognitive impairments that are sensitive to rapamycin treatment, suggesting potential therapeutic approaches 4. The severity can range from moderate intellectual disability to severe epileptic encephalopathy with status epilepticus 7.

Sources cited
1
KPTN is part of KICSTOR complex that negatively regulates mTORC1 and recruits GATOR1 to lysosomes
PMID: 28199306
2
Structural organization of KICSTOR showing SZT2 scaffold binding ITFG2-KPTN heterodimer and positioning GATOR1
PMID: 41198956
3
FBXO2-mediated ubiquitination of KPTN disrupts KICSTOR function and promotes mTORC1 signaling
PMID: 41401028
4
KPTN mutations cause brain overgrowth, cognitive deficits, and hyperactive mTORC1 signaling responsive to rapamycin
PMID: 37437211
5
KPTN mutations cause autosomal recessive intellectual developmental disorder 41 with epilepsy
PMID: 36703628
6
KPTN mutations cause macrocephaly and intellectual disability syndrome
PMID: 25847626
7
KPTN deficiency can cause severe epileptic phenotypes including status epilepticus
PMID: 32358097
Disease Associationsβ“˜21
macrocephaly-developmental delay syndromeOpen Targets
0.79Strong
genetic disorderOpen Targets
0.47Moderate
complex neurodevelopmental disorderOpen Targets
0.37Weak
brain aneurysmOpen Targets
0.24Weak
craniosynostosisOpen Targets
0.18Weak
Immunodeficiency due to a late component of complements deficiencyOpen Targets
0.07Suggestive
mannose-binding lectin deficiencyOpen Targets
0.06Suggestive
recurrent Neisseria infections due to factor D deficiencyOpen Targets
0.05Suggestive
immunodeficiency 28Open Targets
0.05Suggestive
Mendelian susceptibility to mycobacterial diseases due to complete IFNgammaR2 deficiencyOpen Targets
0.05Suggestive
immunodeficiency 31BOpen Targets
0.05Suggestive
Susceptibility to viral and mycobacterial infectionsOpen Targets
0.05Suggestive
Autosomal recessive hyper-IgE syndromeOpen Targets
0.05Suggestive
Autosomal recessive hyper-IgE syndrome due to TYK2 deficiencyOpen Targets
0.05Suggestive
immunodeficiency 35Open Targets
0.05Suggestive
type II complement component 8 deficiencyOpen Targets
0.05Suggestive
Immunodeficiency due to interleukin-1 receptor-associated kinase-4 deficiencyOpen Targets
0.04Suggestive
MODYOpen Targets
0.04Suggestive
autosomal recessive severe congenital neutropenia due to JAGN1 deficiencyOpen Targets
0.04Suggestive
intellectual developmental disorder, X-linked 114Open Targets
0.04Suggestive
Intellectual developmental disorder, autosomal recessive 41UniProt
Pathogenic Variants22
NM_007059.4(KPTN):c.714_731dup (p.Gln246_Asp247insMetTrpSerValLeuGln)Pathogenic
Macrocephaly-developmental delay syndrome|not provided|Inborn genetic diseases|KPTN-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 246
NM_007059.4(KPTN):c.184dup (p.Ile62fs)Pathogenic
not provided|See cases|Macrocephaly-developmental delay syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 62
NM_007059.4(KPTN):c.776C>A (p.Ser259Ter)Pathogenic
Macrocephaly-developmental delay syndrome|not provided|Inborn genetic diseases|KPTN-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 259
NM_007059.4(KPTN):c.597_598dup (p.Ser200fs)Pathogenic
not provided|Macrocephaly-developmental delay syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 200
NM_007059.4(KPTN):c.394+1G>TPathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2026
NM_007059.4(KPTN):c.999+1G>TLikely pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2026
NM_007059.4(KPTN):c.777_783dup (p.Lys262fs)Pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 262
NM_007059.4(KPTN):c.600-1G>TLikely pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2025
NM_007059.4(KPTN):c.599+1G>TPathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2025
NM_007059.4(KPTN):c.644_653dup (p.Leu219fs)Pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 219
NM_007059.4(KPTN):c.309+1G>ALikely pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2024
NM_007059.3(KPTN):c.397_398delAGPathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2023
NM_007059.4(KPTN):c.391del (p.Ala131fs)Pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 131
NM_007059.4(KPTN):c.736C>T (p.Gln246Ter)Pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 246
NM_007059.4(KPTN):c.599+1G>APathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2022
NM_007059.4(KPTN):c.1183-1G>APathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2022
NM_007059.4(KPTN):c.863G>C (p.Arg288Pro)Likely pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2022β†’ Residue 288
NM_007059.4(KPTN):c.785_786del (p.Lys262fs)Pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2021β†’ Residue 262
NM_007059.4(KPTN):c.754C>T (p.Arg252Ter)Likely pathogenic
Macrocephaly-developmental delay syndrome
β˜…β˜†β˜†β˜†2020β†’ Residue 252
NM_007059.4(KPTN):c.692del (p.Val231fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 231
View on ClinVar β†—
Related Genes
LAMP1Protein interaction100%RRAGBProtein interaction100%SAMTORProtein interaction100%WDR24Protein interaction100%MIOSProtein interaction83%SEH1LProtein interaction81%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
77%
Brain
57%
Heart
53%
Lung
50%
Ovary
37%
Gene Interaction Network
Click a node to explore
KPTNLAMP1RRAGBSAMTORWDR24MIOSSEH1L
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9Y664
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.99LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.75 [0.57–0.99]
RankingsWhere KPTN stands among ~20K protein-coding genes
  • #12,376of 20,598
    Most Researched28
  • #2,118of 5,498
    Most Pathogenic Variants22
  • #9,475of 17,882
    Most Constrained (LOEUF)0.99
Genes detectedKPTN
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1.
PMID: 28199306
Nature Β· 2017
1.00
2
FBXO2-mediated KPTN ubiquitination promotes amino acid-dependent mTORC1 signaling and tumor growth.
PMID: 41401028
J Clin Invest Β· 2026
0.90
3
Architecture of the human KICSTOR and GATOR1-KICSTOR complexes.
PMID: 41198956
Nat Struct Mol Biol Β· 2025
0.80
4
Models of KPTN-related disorder implicate mTOR signalling in cognitive and overgrowth phenotypes.
PMID: 37437211
Brain Β· 2023
0.70
5
Bi-allelic KICS2 mutations impair KICSTOR complex-mediated mTORC1 regulation, causing intellectual disability and epilepsy.
PMID: 39824192
Am J Hum Genet Β· 2025
0.60