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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCYL1
SCY1 like pseudokinase 1
Chromosome 11 Β· 11q13.1
NCBI Gene: 57410Ensembl: ENSG00000142186.18HGNC: HGNC:14372UniProt: E9PK59
112PubMed Papers
21Diseases
0Drugs
34Pathogenic Variants
FUNCTIONAL ROLE
Transcription FactorTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cis-Golgi networkcytosolmembraneCOPI vesicle coatacute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndromeautosomal recessive cerebellar ataxiagenetic disorderneuroinflammatory disorder
✦AI Summary

SCYL1 is a pseudokinase that functions as a transcriptional activator and regulator of intracellular membrane trafficking 1. It localizes to multiple cellular compartments including the Golgi apparatus, endoplasmic reticulum-Golgi intermediate compartment, and centrosomes, where it regulates vesicular transport and protein secretion 2. Mechanistically, SCYL1 is phosphorylated by mTORC1 at Ser754, controlling Golgi architecture and extracellular vesicle secretion; dephosphorylation leads to endosomal redistribution and altered secretory function 3. In cancer contexts, SCYL1 promotes malignancy through distinct pathways: it activates mTORC1 signaling to inhibit autophagy and promote gastric cancer metastasis 4, and its overexpression is associated with poor prognosis in breast cancer 1. Loss-of-function SCYL1 mutations cause acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome (CALFAN), characterized by progressive cholestasis and multisystem involvement due to impaired vesicular trafficking and increased endoplasmic reticulum stress 2. SCYL1 also maintains motor neuron viability through overlapping redundancy with SCYL3, regulating TDP-43 proteostasis 5. These findings position SCYL1 as both an oncogenic target and a critical regulator of organ-specific secretory function.

Sources cited
1
SCYL1 activates mTORC1 signaling pathway, inhibits autophagy, and promotes gastric cancer metastasis
PMID: 39394539
2
SCYL1-BP1 interacts with Cyclin F to regulate cell cycle progression and affects hepatocellular carcinoma
PMID: 25980818
3
SCYL1 deficiency causes recurrent acute liver failure with progressive cholestasis and involves impaired vesicular trafficking
PMID: 38279772
4
SCYL1 overexpression is associated with poor prognosis and promotes breast cancer progression
PMID: 36290821
5
SCYL1 pathogenic variants cause recurrent liver failure in childhood, even without typical phenotypic features
PMID: 32146038
6
SCYL1 and SCYL3 work together to maintain motor neuron viability and regulate TDP-43 proteostasis
PMID: 29437892
7
SCYL1 variants cause autosomal recessive cerebellar ataxia with liver failure and growth retardation through aberrant splicing
PMID: 30258122
8
mTORC1 phosphorylates SCYL1 at Ser754 to control Golgi localization, architecture, and extracellular vesicle secretion
PMID: 35948564
Disease Associationsβ“˜21
acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndromeOpen Targets
0.77Strong
autosomal recessive cerebellar ataxiaOpen Targets
0.56Moderate
genetic disorderOpen Targets
0.52Moderate
neuroinflammatory disorderOpen Targets
0.24Weak
Alzheimer diseaseOpen Targets
0.23Weak
Parkinson diseaseOpen Targets
0.21Weak
neurodegenerative diseaseOpen Targets
0.21Weak
multiple sclerosisOpen Targets
0.21Weak
lysosomal storage diseaseOpen Targets
0.21Weak
breast cancerOpen Targets
0.11Weak
neoplasmOpen Targets
0.10Suggestive
hepatocellular carcinomaOpen Targets
0.08Suggestive
lung cancerOpen Targets
0.08Suggestive
gastric cancerOpen Targets
0.08Suggestive
diabetes mellitusOpen Targets
0.08Suggestive
chronic obstructive pulmonary diseaseOpen Targets
0.08Suggestive
Proximal spinal muscular atrophy type 4Open Targets
0.07Suggestive
spinal muscular atrophy, type IVOpen Targets
0.07Suggestive
psoriatic arthritisOpen Targets
0.07Suggestive
familial amyotrophic lateral sclerosisOpen Targets
0.07Suggestive
Spinocerebellar ataxia, autosomal recessive, 21UniProt
Pathogenic Variants34
NM_020680.4(SCYL1):c.526A>T (p.Lys176Ter)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome|SCYL1-related disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 176
NM_020680.4(SCYL1):c.1567C>T (p.Arg523Ter)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 523
NM_020680.4(SCYL1):c.1841_1842del (p.Pro614fs)Likely pathogenic
not provided|Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 614
NM_020680.4(SCYL1):c.459C>T (p.Gly153=)Likely pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 153
NM_020680.4(SCYL1):c.1386+1G>TPathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜…β˜†β˜†2023
NM_020680.4(SCYL1):c.1021del (p.Phe340_Leu341insTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 340
NM_020680.4(SCYL1):c.3G>A (p.Met1Ile)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 1
NM_020680.4(SCYL1):c.1173_1174dup (p.His392fs)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 392
NM_020680.4(SCYL1):c.2094dup (p.Glu699Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 699
NM_020680.4(SCYL1):c.1A>T (p.Met1Leu)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1
NM_020680.4(SCYL1):c.1180del (p.Val394fs)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 394
NM_020680.4(SCYL1):c.60_70del (p.Glu22fs)Likely pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 22
NM_020680.4(SCYL1):c.1117-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_020680.4(SCYL1):c.476del (p.Gly159fs)Likely pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 159
NM_020680.4(SCYL1):c.1386+1G>APathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2023
NM_020680.4(SCYL1):c.1591_1610del (p.Arg531fs)Likely pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 531
NM_020680.4(SCYL1):c.1230+1G>ALikely pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome|not provided
β˜…β˜†β˜†β˜†2023
NM_020680.4(SCYL1):c.2031+1G>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2022
NM_020680.4(SCYL1):c.560del (p.Pro187fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2021β†’ Residue 187
NM_020680.4(SCYL1):c.451C>T (p.Arg151Ter)Pathogenic
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
β˜…β˜†β˜†β˜†2019β†’ Residue 151
View on ClinVar β†—
Related Genes
GORABProtein interaction99%ARCN1Protein interaction90%COPAProtein interaction90%COPB1Protein interaction90%COPB2Protein interaction90%COPEProtein interaction90%
Tissue Expression6 tissues
Liver
100%
Lung
82%
Ovary
81%
Heart
75%
Bone Marrow
48%
Brain
44%
Gene Interaction Network
Click a node to explore
SCYL1GORABARCN1COPACOPB1COPB2COPE
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96KG9
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.16LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.97 [0.81–1.16]
RankingsWhere SCYL1 stands among ~20K protein-coding genes
  • #4,244of 20,598
    Most Researched112 Β· top quartile
  • #1,699of 5,498
    Most Pathogenic Variants34
  • #12,090of 17,882
    Most Constrained (LOEUF)1.16
Genes detectedSCYL1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
SCYL1-mediated regulation of the mTORC1 signaling pathway inhibits autophagy and promotes gastric cancer metastasis.
PMID: 39394539
J Cancer Res Clin Oncol Β· 2024
1.00
2
SCYL1-BP1 affects cell cycle arrest in human hepatocellular carcinoma cells via Cyclin F and RRM2.
PMID: 25980818
Anticancer Agents Med Chem Β· 2016
0.90
3
Disorders of vesicular trafficking presenting with recurrent acute liver failure: NBAS, RINT1, and SCYL1 deficiency.
PMID: 38279772
J Inherit Metab Dis Β· 2025
0.80
4
Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
PMID: 36290821
Curr Oncol Β· 2022
0.70
5
Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
PMID: 32146038
Arch Pediatr Β· 2020
0.60