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Aliases for TM4SF20 Gene

Aliases for TM4SF20 Gene

  • Transmembrane 4 L Six Family Member 20 2 3 5
  • Transmembrane 4 L6 Family Member 20 3
  • TCCE518 3
  • PRO994 3
  • SLI5 3

External Ids for TM4SF20 Gene

Previous GeneCards Identifiers for TM4SF20 Gene

  • GC02M228053
  • GC02M227935
  • GC02M228226
  • GC02M220071

Summaries for TM4SF20 Gene

Entrez Gene Summary for TM4SF20 Gene

  • The protein encoded by this gene is a member of the four-transmembrane L6 superfamily. Members of this family function in various cellular processes including cell proliferation, motility, and adhesion via their interactions with integrins. In human brain tissue, this gene is expressed at high levels in the parietal lobe, occipital lobe, hippocampus, pons, white matter, corpus callosum, and cerebellum. Knockout of the homologous gene in mouse results in a neurobehavioral phenotype with suggested enhanced motor coordination. A deletion mutation in the human gene is associated with specific language impairment-5. [provided by RefSeq, Jul 2016]

GeneCards Summary for TM4SF20 Gene

TM4SF20 (Transmembrane 4 L Six Family Member 20) is a Protein Coding gene. Diseases associated with TM4SF20 include Specific Language Impairment 5 and Specific Language Impairment.

UniProtKB/Swiss-Prot for TM4SF20 Gene

  • Polytopic transmembrane protein that inhibits regulated intramembrane proteolysis (RIP) of CREB3L1, inhibiting its activation and the induction of collagen synthesis (PubMed:25310401, PubMed:27499293). In response to ceramide, which alters TM4SF20 membrane topology, stimulates RIP activation of CREB3L1 (PubMed:27499293). Ceramide reverses the direction through which transmembrane helices are translocated into the endoplasmic reticulum membrane during translation of TM4SF20, this mechanism is called regulated alternative translocation (RAT) and regulates the function of the transmembrane protein (PubMed:27499293).

Additional gene information for TM4SF20 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TM4SF20 Gene

Genomics for TM4SF20 Gene

Regulatory Elements for TM4SF20 Gene

Enhancers for TM4SF20 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H227384 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.1 -5.2 -5223 6 HDAC1 PKNOX1 TAL1 MAX SIN3A EBF1 BRCA1 RFX5 TCF12 EED AGFG1 TM4SF20 MFF CCL20 ENSG00000284629
GH02H227461 1.9 FANTOM5 Ensembl ENCODE dbSUPER 9.6 -83.4 -83419 7 PKNOX1 ATF1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF121 GLIS2 ZNF207 TM4SF20 AGFG1 MIR5703 ENSG00000284629
GH02H227404 1.3 Ensembl ENCODE 13.8 -24.5 -24518 3 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 FOS TM4SF20 AGFG1 ENSG00000284629 MIR5703
GH02H227414 1.4 FANTOM5 Ensembl ENCODE 10 -33.9 -33931 3 SOX13 JUN BACH1 MAX ZIC2 ZNF644 RARA TEAD3 ZNF316 LCORL AGFG1 TM4SF20 CCL20 ENSG00000284629 MIR5703
GH02H227429 0.8 ENCODE 16.6 -48.5 -48483 2 SOX13 FOXA2 MAX CEBPG RAD21 YY1 NR2F6 TCF7L2 GATAD2A SOX5 AGFG1 TM4SF20 MFF ENSG00000284629 MIR5703
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TM4SF20 on UCSC Golden Path with GeneCards custom track

Genomic Location for TM4SF20 Gene

Chromosome:
2
Start:
227,362,156 bp from pter
End:
227,381,995 bp from pter
Size:
19,840 bases
Orientation:
Minus strand

Genomic View for TM4SF20 Gene

Genes around TM4SF20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TM4SF20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TM4SF20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TM4SF20 Gene

Proteins for TM4SF20 Gene

  • Protein details for TM4SF20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q53R12-T4S20_HUMAN
    Recommended name:
    Transmembrane 4 L6 family member 20
    Protein Accession:
    Q53R12
    Secondary Accessions:
    • B2RP42
    • Q5U609
    • Q6UWS1
    • Q9H5X9

    Protein attributes for TM4SF20 Gene

    Size:
    229 amino acids
    Molecular mass:
    25075 Da
    Quaternary structure:
    No Data Available

neXtProt entry for TM4SF20 Gene

Post-translational modifications for TM4SF20 Gene

  • Cleaved by signal peptidase at Ser-14 but the peptide does not act as a signal peptide. Cleavage is inhibited by ceramide which inverts the orientation of TM4SF20 in membranes exposing the N-terminus to the cytosol and not to the endoplasmic reticulum lumen.
  • Glycosylated at Asn-132, Asn-148 and Asn-163 in presence of ceramide which inverts the orientation of TM4SF20 in membranes exposing these residues to the endoplasmic reticulum lumen.

Other Protein References for TM4SF20 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TM4SF20 Gene

Domains & Families for TM4SF20 Gene

Gene Families for TM4SF20 Gene

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

Protein Domains for TM4SF20 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TM4SF20 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q53R12

UniProtKB/Swiss-Prot:

T4S20_HUMAN :
  • The first transmembrane helix plays a critical role for the insertion orientation in the endoplasmic reticulum membrane.
  • Belongs to the L6 tetraspanin family.
Domain:
  • The first transmembrane helix plays a critical role for the insertion orientation in the endoplasmic reticulum membrane.
Family:
  • Belongs to the L6 tetraspanin family.
genes like me logo Genes that share domains with TM4SF20: view

Function for TM4SF20 Gene

Molecular function for TM4SF20 Gene

UniProtKB/Swiss-Prot Function:
Polytopic transmembrane protein that inhibits regulated intramembrane proteolysis (RIP) of CREB3L1, inhibiting its activation and the induction of collagen synthesis (PubMed:25310401, PubMed:27499293). In response to ceramide, which alters TM4SF20 membrane topology, stimulates RIP activation of CREB3L1 (PubMed:27499293). Ceramide reverses the direction through which transmembrane helices are translocated into the endoplasmic reticulum membrane during translation of TM4SF20, this mechanism is called regulated alternative translocation (RAT) and regulates the function of the transmembrane protein (PubMed:27499293).
UniProtKB/Swiss-Prot Induction:
TGFB1 inhibits TM4SF20 expression to activate CREB3L1 (PubMed:25310401).
genes like me logo Genes that share phenotypes with TM4SF20: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TM4SF20

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TM4SF20
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TM4SF20 Gene

Localization for TM4SF20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TM4SF20 Gene

Membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass membrane protein. Note=Ceramide alters the direction through which transmembrane helices are translocated into the endoplasmic reticulum membrane during translation of TM4SF20. {ECO:0000269 PubMed:27499293}.

Subcellular locations from

COMPARTMENTS
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 TM4SF20 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Focal adhesion sites (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TM4SF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane IEA,IDA 27499293
GO:0005886 plasma membrane IDA --
GO:0005925 focal adhesion IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA --
genes like me logo Genes that share ontologies with TM4SF20: view

Pathways & Interactions for TM4SF20 Gene

SuperPathways for TM4SF20 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TM4SF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045861 negative regulation of proteolysis IDA 25310401
genes like me logo Genes that share ontologies with TM4SF20: view

No data available for Pathways by source and SIGNOR curated interactions for TM4SF20 Gene

Drugs & Compounds for TM4SF20 Gene

No Compound Related Data Available

Transcripts for TM4SF20 Gene

mRNA/cDNA for TM4SF20 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TM4SF20 Gene

Transmembrane 4 L six family member 20:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TM4SF20
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for TM4SF20 Gene

No ASD Table

Relevant External Links for TM4SF20 Gene

GeneLoc Exon Structure for
TM4SF20
ECgene alternative splicing isoforms for
TM4SF20

Expression for TM4SF20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TM4SF20 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TM4SF20 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x48.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TM4SF20 Gene



NURSA nuclear receptor signaling pathways regulating expression of TM4SF20 Gene:

TM4SF20

SOURCE GeneReport for Unigene cluster for TM4SF20 Gene:

Hs.156652

mRNA Expression by UniProt/SwissProt for TM4SF20 Gene:

Q53R12-T4S20_HUMAN
Tissue specificity: Expressed in the brain, with high levels in the parietal lobe, hippocampus, pons, white matter and cerebellum.

Evidence on tissue expression from TISSUES for TM4SF20 Gene

  • Intestine(4.1)
genes like me logo Genes that share expression patterns with TM4SF20: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for TM4SF20 Gene

Orthologs for TM4SF20 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TM4SF20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TM4SF20 33 34
  • 99.71 (n)
mouse
(Mus musculus)
Mammalia Tm4sf20 33 16 34
  • 83.19 (n)
dog
(Canis familiaris)
Mammalia TM4SF20 33 34
  • 82.82 (n)
cow
(Bos Taurus)
Mammalia TM4SF20 33 34
  • 82.68 (n)
rat
(Rattus norvegicus)
Mammalia Tm4sf20 33
  • 78.76 (n)
oppossum
(Monodelphis domestica)
Mammalia TM4SF20 34
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TM4SF20 34
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tm4sf20 33
  • 54.24 (n)
Species where no ortholog for TM4SF20 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • zebrafish (Danio rerio)

Evolution for TM4SF20 Gene

ENSEMBL:
Gene Tree for TM4SF20 (if available)
TreeFam:
Gene Tree for TM4SF20 (if available)

Paralogs for TM4SF20 Gene

No data available for Paralogs for TM4SF20 Gene

Variants for TM4SF20 Gene

Sequence variations from dbSNP and Humsavar for TM4SF20 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000020956 -- 227,371,545(+) ACTCT(C/G)TTGCC intron-variant
rs1000116361 -- 227,375,674(+) TTAGT(A/G)GAGAC intron-variant
rs1000154586 -- 227,375,527(+) CTCTG(C/T)CACCT intron-variant
rs1000344491 -- 227,380,843(+) GGGGG(C/T)GCACA upstream-variant-2KB
rs1000446544 -- 227,375,226(+) TGGCC(-/A)AAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TM4SF20 Gene

Variant ID Type Subtype PubMed ID
dgv1217e212 CNV gain 25503493
esv23388 CNV gain 19812545
esv2421896 CNV duplication 20811451
esv2721559 CNV deletion 23290073
esv3302868 CNV tandem duplication 20981092
esv3575336 CNV gain 25503493
esv3594534 CNV loss 21293372
esv3594535 CNV loss 21293372
esv3594536 CNV gain 21293372
nsv518519 CNV gain 19592680
nsv522790 CNV loss 19592680
nsv584594 CNV gain 21841781
nsv584607 CNV gain 21841781

Variation tolerance for TM4SF20 Gene

Residual Variation Intolerance Score: 82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.12; 38.67% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TM4SF20 Gene

Human Gene Mutation Database (HGMD)
TM4SF20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TM4SF20

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TM4SF20 Gene

Disorders for TM4SF20 Gene

MalaCards: The human disease database

(3) MalaCards diseases for TM4SF20 Gene - From: HGMD, OMIM, ClinVar, and GeneCards

Disorder Aliases PubMed IDs
specific language impairment 5
  • sli5
specific language impairment
autism spectrum disorder
  • pervasive developmental disorder
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

T4S20_HUMAN
  • Specific language impairment 5 (SLI5) [MIM:615432]: A disorder characterized by a delay in early speech acquisition. It is usually associated with cerebral white matter abnormalities on brain MRI. Some individuals may show disorders in communication, consistent with autism spectrum disorder, or global developmental delay, although others ultimately show normal cognitive function. Penetrance is incomplete and expressivity is variable. {ECO:0000269 PubMed:23810381}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TM4SF20

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TM4SF20
genes like me logo Genes that share disorders with TM4SF20: view

No data available for Genatlas for TM4SF20 Gene

Publications for TM4SF20 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 60
  2. Inverting the Topology of a Transmembrane Protein by Regulating the Translocation of the First Transmembrane Helix. (PMID: 27499293) Chen Q … Ye J (Molecular cell 2016) 3 4 60
  3. Sustained induction of collagen synthesis by TGF-β requires regulated intramembrane proteolysis of CREB3L1. (PMID: 25310401) Chen Q … Ye J (PloS one 2014) 3 4 60
  4. TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. (PMID: 23810381) Wiszniewski W … Lalani SR (American journal of human genetics 2013) 3 4 60
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 60

Products for TM4SF20 Gene

Sources for TM4SF20 Gene

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