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Aliases for SIL1 Gene

Aliases for SIL1 Gene

  • SIL1 Nucleotide Exchange Factor 2 3 5
  • BiP-Associated Protein 3 4
  • BAP 3 4
  • SIL1 Homolog, Endoplasmic Reticulum Chaperone (S. Cerevisiae) 2
  • SIL1-Like Protein Endoplasmic Reticulum Chaperone 3
  • SIL1 Homolog, Endoplasmic Reticulum Chaperone 3
  • Nucleotide Exchange Factor SIL1 3
  • Marinesco-Sjogren Syndrome 2
  • ULG5 3
  • MSS 3

External Ids for SIL1 Gene

Previous HGNC Symbols for SIL1 Gene

  • MSS

Previous GeneCards Identifiers for SIL1 Gene

  • GC05M138157
  • GC05M138313
  • GC05M138358
  • GC05M138310
  • GC05M133472
  • GC05M138282

Summaries for SIL1 Gene

Entrez Gene Summary for SIL1 Gene

  • This gene encodes a resident endoplasmic reticulum (ER), N-linked glycoprotein with an N-terminal ER targeting sequence, 2 putative N-glycosylation sites, and a C-terminal ER retention signal. This protein functions as a nucleotide exchange factor for another unfolded protein response protein. Mutations in this gene have been associated with Marinesco-Sjogren syndrome. Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for SIL1 Gene

SIL1 (SIL1 Nucleotide Exchange Factor) is a Protein Coding gene. Diseases associated with SIL1 include Marinesco-Sjogren Syndrome and Sjogren Syndrome. Among its related pathways are Protein processing in endoplasmic reticulum. Gene Ontology (GO) annotations related to this gene include binding and unfolded protein binding.

UniProtKB/Swiss-Prot for SIL1 Gene

  • Required for protein translocation and folding in the endoplasmic reticulum (ER). Functions as a nucleotide exchange factor for the ER lumenal chaperone HSPA5.

Gene Wiki entry for SIL1 Gene

Additional gene information for SIL1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIL1 Gene

Genomics for SIL1 Gene

GeneHancer (GH) Regulatory Elements for SIL1 Gene

Promoters and enhancers for SIL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J139292 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -1.3 -1285 3.8 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 ZNF610 ZNF585B GLIS1 SIL1 MATR3 KDM3B PURA DNAJC18 ENSG00000232174 LOC101929719 GC05P139300 ENSG00000280987 GC05P138946
GH05J139196 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.2 +95.8 95787 2.7 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B SIL1 KDM3B CDC23 RPL7P19 RNU6-572P GC05P139163 GC05P139162 GC05P138946
GH05J139381 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11 -96.2 -96161 15.5 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 SLC23A1 MZB1 DNAJC18 PURA PAIP2 SIL1 MATR3 PROB1 GC05P139382 SPATA24
GH05J139341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.6 -48.8 -48758 2.6 MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 ZNF610 PAIP2 PURA KDM3B RPL7P19 ENSG00000232174 SLC23A1 MZB1 PROB1 MATR3 SNORA74A
GH05J139147 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.2 +144.5 144466 4 HDAC1 PKNOX1 RAD21 ZNF335 TCF12 RCOR1 FOS CREM SMARCA5 RXRA LOC105379194 CTNNA1 MATR3 SIL1 GC05P139162 GC05P139163 GC05P139102 GC05P139106 GC05P139105 GC05P139104
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SIL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SIL1 gene promoter:
  • STAT1
  • Meis-1b
  • Meis-1
  • HOXA9B
  • HOXA9
  • POU2F1
  • POU2F1a

Genomic Locations for SIL1 Gene

Genomic Locations for SIL1 Gene
346,838 bases
Minus strand
346,838 bases
Minus strand

Genomic View for SIL1 Gene

Genes around SIL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIL1 Gene

Proteins for SIL1 Gene

  • Protein details for SIL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Nucleotide exchange factor SIL1
    Protein Accession:
    Secondary Accessions:
    • D3DQC2
    • Q8N2L3

    Protein attributes for SIL1 Gene

    461 amino acids
    Molecular mass:
    52085 Da
    Quaternary structure:
    • Interacts with HSPA5.

neXtProt entry for SIL1 Gene

Post-translational modifications for SIL1 Gene

  • N-glycosylated.
  • Glycosylation at isoforms=236, posLast=193193, posLast=127127, isoforms=97, and isoforms=41
  • Ubiquitination at isoforms=309
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SIL1 Gene

Domains & Families for SIL1 Gene

Gene Families for SIL1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SIL1 Gene


Suggested Antigen Peptide Sequences for SIL1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SIL1 family.
  • Belongs to the SIL1 family.
genes like me logo Genes that share domains with SIL1: view

Function for SIL1 Gene

Molecular function for SIL1 Gene

UniProtKB/Swiss-Prot Function:
Required for protein translocation and folding in the endoplasmic reticulum (ER). Functions as a nucleotide exchange factor for the ER lumenal chaperone HSPA5.

Phenotypes From GWAS Catalog for SIL1 Gene

Gene Ontology (GO) - Molecular Function for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000774 adenyl-nucleotide exchange factor activity IBA --
GO:0005515 protein binding IPI 25416956
GO:0051082 unfolded protein binding NAS 11101517
genes like me logo Genes that share ontologies with SIL1: view
genes like me logo Genes that share phenotypes with SIL1: view

Human Phenotype Ontology for SIL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for SIL1 Gene

miRTarBase miRNAs that target SIL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SIL1 Gene

Localization for SIL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIL1 Gene

Endoplasmic reticulum lumen.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SIL1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
nucleus 2
mitochondrion 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 16502470
GO:0005737 cytoplasm IBA --
GO:0005783 endoplasmic reticulum NAS,IBA 11101517
GO:0005788 endoplasmic reticulum lumen IEA --
genes like me logo Genes that share ontologies with SIL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SIL1 Gene

Pathways & Interactions for SIL1 Gene

genes like me logo Genes that share pathways with SIL1: view

Pathways by source for SIL1 Gene

1 KEGG pathway for SIL1 Gene

Gene Ontology (GO) - Biological Process for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006457 protein folding NAS 11101517
GO:0006886 intracellular protein transport NAS 11101517
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with SIL1: view

No data available for SIGNOR curated interactions for SIL1 Gene

Drugs & Compounds for SIL1 Gene

(1) Drugs for SIL1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SIL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SIL1: view

Transcripts for SIL1 Gene

Unigene Clusters for SIL1 Gene

SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SIL1 Gene

No ASD Table

Relevant External Links for SIL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SIL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SIL1 Gene

Protein differential expression in normal tissues from HIPED for SIL1 Gene

This gene is overexpressed in Milk (29.5) and Testis (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SIL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SIL1 Gene:


SOURCE GeneReport for Unigene cluster for SIL1 Gene:


mRNA Expression by UniProt/SwissProt for SIL1 Gene:

Tissue specificity: Highly expressed in tissues which produce large amounts of secreted proteins such as kidney, liver and placenta. Also expressed in colon, heart, lung, ovary, pancreas, peripheral leukocyte, prostate, spleen and thymus. Expressed at low levels throughout the brain.

Evidence on tissue expression from TISSUES for SIL1 Gene

  • Skin(4.5)
  • Liver(4.4)
  • Intestine(3.4)
  • Lung(3.1)
  • Nervous system(2.8)
  • Lymph node(2.6)
  • Muscle(2.4)
  • Stomach(2.3)
  • Thyroid gland(2.3)
  • Blood(2.2)
  • Heart(2.1)
  • Gall bladder(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SIL1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • pituitary gland
  • skull
  • breast
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shoulder
  • thigh
  • toe
  • ulna
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SIL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for SIL1 Gene

Orthologs for SIL1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SIL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SIL1 34 33
  • 99.19 (n)
(Canis familiaris)
Mammalia SIL1 34 33
  • 89.57 (n)
(Bos Taurus)
Mammalia SIL1 34 33
  • 87.26 (n)
(Rattus norvegicus)
Mammalia Sil1 33
  • 85.39 (n)
(Mus musculus)
Mammalia Sil1 16 34 33
  • 84.96 (n)
(Monodelphis domestica)
Mammalia SIL1 34
  • 70 (a)
(Ornithorhynchus anatinus)
Mammalia SIL1 34
  • 50 (a)
(Gallus gallus)
Aves SIL1 34 33
  • 67.61 (n)
(Anolis carolinensis)
Reptilia SIL1 34
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sil1 33
  • 56.95 (n)
(Danio rerio)
Actinopterygii LOC568308 33
  • 58.25 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003488 33
  • 48.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10420 34 35 33
  • 45.71 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SIL1 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
Species where no ortholog for SIL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SIL1 Gene

Gene Tree for SIL1 (if available)
Gene Tree for SIL1 (if available)
Evolutionary constrained regions (ECRs) for SIL1: view image

Paralogs for SIL1 Gene

No data available for Paralogs for SIL1 Gene

Variants for SIL1 Gene

Sequence variations from dbSNP and Humsavar for SIL1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs11555154 benign, likely-benign, not specified, Marinesco-Sj\u00f6gren syndrome 139,127,849(-) G/C 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs115800498 conflicting-interpretations-of-pathogenicity, likely-benign, not specified, not provided, Marinesco-Sj\u00f6gren syndrome 139,042,705(-) G/A coding_sequence_variant, missense_variant
rs119456965 pathogenic, Marinesco-Sj\u00f6gren syndrome 139,050,960(-) G/A coding_sequence_variant, stop_gained
rs119456966 pathogenic, Marinesco-Sj\u00f6gren syndrome, not provided 138,947,191(-) G/A coding_sequence_variant, stop_gained
rs119456967 pathogenic, Marinesco-Sj\u00f6gren syndrome 138,947,133(-) A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for SIL1 Gene

Variant ID Type Subtype PubMed ID
esv2666199 CNV deletion 23128226
esv2672987 CNV deletion 23128226
esv3408136 CNV insertion 20981092
esv3447133 CNV duplication 20981092
esv3566707 CNV deletion 23714750
esv3566709 CNV deletion 23714750
esv3606932 CNV loss 21293372
esv3606933 CNV loss 21293372
esv3606935 CNV gain 21293372
esv3606936 CNV loss 21293372
nsv1017883 CNV gain 25217958
nsv1029030 CNV gain 25217958
nsv1137028 CNV deletion 24896259
nsv1140572 CNV deletion 24896259
nsv436490 CNV deletion 17901297
nsv5027 CNV insertion 18451855
nsv950408 CNV deletion 24416366
nsv968249 CNV duplication 23825009

Variation tolerance for SIL1 Gene

Residual Variation Intolerance Score: 74.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.99; 60.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SIL1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIL1 Gene

Disorders for SIL1 Gene

MalaCards: The human disease database

(14) MalaCards diseases for SIL1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
marinesco-sjogren syndrome
  • mss
sjogren syndrome
  • sicca syndrome
spindle cell synovial sarcoma
  • synovial sarcoma with spindle cell components
dandy-walker syndrome
  • dws
gastric papillary adenocarcinoma
  • papillary adenocarcinoma of stomach
- elite association - COSMIC cancer census association via MalaCards
Search SIL1 in MalaCards View complete list of genes associated with diseases


  • Marinesco-Sjoegren syndrome (MSS) [MIM:248800]: Autosomal recessive multisystem disorder which is characterized by cerebellar ataxia due to cerebellar atrophy, with Purkinje and granule cell loss and myopathy featuring marked muscle replacement with fat and connective tissue. Other cardinal features include bilateral cataracts, hypergonadotrophic hypogonadism and mild to severe mental retardation. Skeletal abnormalities, short stature, dysarthria, strabismus and nystagmus are also frequent findings. Mutational inactivation of this protein may result in ER stress-induced cell death signaling or malfunctioning chaperone machineries that mishandle client proteins which are critical for the organs targeted in MSS. {ECO:0000269 PubMed:16282977, ECO:0000269 PubMed:16282978}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SIL1

genes like me logo Genes that share disorders with SIL1: view

No data available for Genatlas for SIL1 Gene

Publications for SIL1 Gene

  1. Mutations in SIL1 cause Marinesco-Sjögren syndrome, a cerebellar ataxia with cataract and myopathy. (PMID: 16282977) Senderek J … Zerres K (Nature genetics 2005) 2 3 4 22 58
  2. The gene disrupted in Marinesco-Sjögren syndrome encodes SIL1, an HSPA5 cochaperone. (PMID: 16282978) Anttonen AK … Lehesjoki AE (Nature genetics 2005) 3 4 22 58
  3. BAP, a mammalian BiP-associated protein, is a nucleotide exchange factor that regulates the ATPase activity of BiP. (PMID: 12356756) Chung KT … Hendershot LM (The Journal of biological chemistry 2002) 2 3 4 58
  4. LHS1 and SIL1 provide a lumenal function that is essential for protein translocation into the endoplasmic reticulum. (PMID: 11101517) Tyson JR … Stirling CJ (The EMBO journal 2000) 2 3 4 58
  5. Novel mutations in the SIL1 gene in a Japanese pedigree with the Marinesco-Sjögren syndrome. (PMID: 20111056) Takahata T … Kitaoka T (Journal of human genetics 2010) 3 22 58

Products for SIL1 Gene

Sources for SIL1 Gene

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