Free for academic non-profit institutions. Other users need a Commercial license

TMEM240 Gene(Protein Coding)

Transmembrane Protein 240

GCID:
GC01M001470
GIFtS:
37
Genes Participants
UDN Logo

Aliases for TMEM240 Gene

Aliases for TMEM240 Gene

  • Transmembrane Protein 240 2 3 3 5
  • C1orf70 3 4
  • Chromosome 1 Open Reading Frame 70 2
  • Transmembrane Protein C1orf70 3
  • Spinocerebellar Ataxia 21 2
  • SCA21 3

External Ids for TMEM240 Gene

Previous HGNC Symbols for TMEM240 Gene

  • C1orf70
  • SCA21

Summaries for TMEM240 Gene

Entrez Gene Summary for TMEM240 Gene

  • This gene encodes a transmembrane-domain containing protein found in the brain and cerebellum. Mutations in this gene result in spinocerebellar ataxia 21. [provided by RefSeq, Dec 2014]

GeneCards Summary for TMEM240 Gene

TMEM240 (Transmembrane Protein 240) is a Protein Coding gene. Diseases associated with TMEM240 include Spinocerebellar Ataxia 21.

Additional gene information for TMEM240 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMEM240 Gene

Genomics for TMEM240 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TMEM240 Gene

Promoters and enhancers for TMEM240 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J001539 Promoter/Enhancer 1 Ensembl ENCODE 650.7 +0.1 111 2.3 MXI1 USF1 POLR2A BACH1 SIN3A REST BCL11B TMEM240 ATAD3B SSU72 ENSG00000272512 GC01M001538 ATAD3A
GH01J000998 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 22.2 +540.0 539964 3.8 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ISG15 HES4 ATAD3B WASH7P INTS11 ENSG00000230092 ENSG00000240731 CDK11A CCNL2 LOC100288379
GH01J001373 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 22.2 +165.3 165330 3.9 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 AURKAIP1 GC01M001374 ENSG00000230092 CDK11A ATAD3B LOC100288379 ENSG00000237094 CCNL2 SDF4 LOC100288069
GH01J001303 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.7 +233.2 233248 6.9 PKNOX1 CLOCK MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 PUSL1 ACAP3 ATAD3B INTS11 ENSG00000240731 SLC35E2A CCNL2 LINC00115 FAAP20 LOC100288379
GH01J001356 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 2.7 +181.1 181082 6.5 HDGF ARNT ARID4B YBX1 DMAP1 ZNF2 FOS SP5 NFYC ZHX2 MXRA8 SLC35E2A LOC100129381 ANKRD65 CCNL2 LOC100288379 SDF4 ENSG00000272455 INTS11 ENSG00000240731
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMEM240 on UCSC Golden Path with GeneCards custom track

Genomic Locations for TMEM240 Gene

Genomic Locations for TMEM240 Gene
chr1:1,534,778-1,540,453
(GRCh38/hg38)
Size:
5,676 bases
Orientation:
Minus strand
chr1:1,470,158-1,475,833
(GRCh37/hg19)
Size:
5,676 bases
Orientation:
Minus strand

Genomic View for TMEM240 Gene

Genes around TMEM240 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMEM240 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMEM240 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TMEM240 Gene

Proteins for TMEM240 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TMEM240 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5SV17-TM240_HUMAN
    Recommended name:
    Transmembrane protein 240
    Protein Accession:
    Q5SV17
    Secondary Accessions:
    • B9EJG7

    Protein attributes for TMEM240 Gene

    Size:
    173 amino acids
    Molecular mass:
    19908 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAI22949.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for TMEM240 Gene

Protein Expression for TMEM240 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TMEM240 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TMEM240 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TMEM240 Gene

Domains & Families for TMEM240 Gene

Gene Families for TMEM240 Gene

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

Protein Domains for TMEM240 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TMEM240 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5SV17

UniProtKB/Swiss-Prot:

TM240_HUMAN :
  • Belongs to the TMEM240 family.
Family:
  • Belongs to the TMEM240 family.
genes like me logo Genes that share domains with TMEM240: view

Function for TMEM240 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes for TMEM240 Gene

GenomeRNAi human phenotypes for TMEM240:
genes like me logo Genes that share phenotypes with TMEM240: view

Human Phenotype Ontology for TMEM240 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TMEM240 Gene

miRTarBase miRNAs that target TMEM240

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMEM240

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for TMEM240 Gene

Localization for TMEM240 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMEM240 Gene

Cell junction, synapse. Cell membrane; Multi-pass membrane protein.

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 TMEM240 gene
Compartment Confidence
plasma membrane 5
extracellular 2

Gene Ontology (GO) - Cellular Components for TMEM240 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
GO:0045202 synapse IEA --
GO:0097060 synaptic membrane ISS --
genes like me logo Genes that share ontologies with TMEM240: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMEM240 Gene

Pathways & Interactions for TMEM240 Gene

SuperPathways for TMEM240 Gene

PathCards logo More details on SuperPathways for TMEM240
No Data Available

Interacting Proteins for TMEM240 Gene

Gene Ontology (GO) - Biological Process for TMEM240 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for TMEM240 Gene

Drugs & Compounds for TMEM240 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for TMEM240 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TMEM240 Gene

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

Unigene Clusters for TMEM240 Gene

Transmembrane protein 240:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMEM240

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMEM240 Gene

No ASD Table

Relevant External Links for TMEM240 Gene

GeneLoc Exon Structure for
TMEM240
ECgene alternative splicing isoforms for
TMEM240

Expression for TMEM240 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMEM240 Gene

mRNA expression in normal human tissues for TMEM240 Gene
mRNA expression by GTEx for TMEM240 GenemRNA expression by BioGPS for TMEM240 Gene

Protein differential expression in normal tissues from HIPED for TMEM240 Gene

This gene is overexpressed in Frontal cortex (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TMEM240 Gene



Protein tissue co-expression partners for TMEM240 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TMEM240 Gene:

TMEM240

SOURCE GeneReport for Unigene cluster for TMEM240 Gene:

Hs.668654

Phenotype-based relationships between genes and organs from Gene ORGANizer for TMEM240 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
Limb:
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with TMEM240: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for TMEM240 Gene

Orthologs for TMEM240 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TMEM240 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia TMEM240 34 33
  • 95.76 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia C16H1orf70 34 33
  • 94.61 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Tmem240 16 34 33
  • 94.41 (n)
rat
(Rattus norvegicus)
 Mammalia Tmem240 33
  • 94.41 (n)
chicken
(Gallus gallus)
 Aves TMEM240 34
  • 87 (a)
 OneToOne
C1ORF70 33
  • 79.96 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 34
  • 82 (a)
 OneToMany
-- 34
  • 44 (a)
 OneToMany
zebrafish
(Danio rerio)
 Actinopterygii tmem240 34
  • 81 (a)
 OneToMany
LOC568378 33
  • 76.69 (n)
TMEM240 (2 of 2) 34
  • 58 (a)
 OneToMany
Species where no ortholog for TMEM240 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TMEM240 Gene

ENSEMBL:
Gene Tree for TMEM240 (if available)
TreeFam:
Gene Tree for TMEM240 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMEM240: view image

Paralogs for TMEM240 Gene

No data available for Paralogs for TMEM240 Gene

Variants for TMEM240 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for TMEM240 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs546291208 Spinocerebellar ataxia 21 (SCA21) [MIM:607454] 1,535,436(-) C/G/T coding_sequence_variant, missense_variant
rs606231451 conflicting-interpretations-of-pathogenicity, pathogenic, Spinocerebellar ataxia 21, not provided, Spinocerebellar ataxia 21 (SCA21) [MIM:607454] 1,535,372(-) G/A coding_sequence_variant, missense_variant
rs606231452 pathogenic, Spinocerebellar ataxia 21 1,535,392(-) G/A/C coding_sequence_variant, stop_gained, synonymous_variant
rs606231453 pathogenic, Spinocerebellar ataxia 21, Spinocerebellar ataxia 21 (SCA21) [MIM:607454] 1,535,616(-) G/A coding_sequence_variant, missense_variant
rs606231454 pathogenic, Spinocerebellar ataxia 21, Spinocerebellar ataxia 21 (SCA21) [MIM:607454] 1,535,723(-) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for TMEM240 Gene

Variant ID Type Subtype PubMed ID
esv2758913 CNV gain+loss 17122850
esv3418946 CNV duplication 20981092
nsv1011818 CNV gain 25217958
nsv10161 CNV gain+loss 18304495
nsv1130940 CNV deletion 24896259
nsv482937 CNV loss 15286789
nsv545000 CNV loss 21841781
nsv950452 CNV deletion 24416366

Variation tolerance for TMEM240 Gene

Gene Damage Index Score: 1.51; 29.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMEM240 Gene

Human Gene Mutation Database (HGMD)
TMEM240
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMEM240

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMEM240 Gene

Disorders for TMEM240 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TMEM240 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia 21
  • sca21
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TM240_HUMAN
  • Spinocerebellar ataxia 21 (SCA21) [MIM:607454]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA21 is characterized by onset in the first decades of life of slowly progressive relatively mild cerebellar ataxia associated with slight extrapyramidal features predominant in older patients and cognitive impairment predominant in younger patients. Note=The disease is caused by mutations affecting the gene represented in this entry. {ECO:0000269 PubMed:25070513}.

Additional Disease Information for TMEM240

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TMEM240: view

No data available for Genatlas for TMEM240 Gene

Publications for TMEM240 Gene

  1. TMEM240 mutations cause spinocerebellar ataxia 21 with mental retardation and severe cognitive impairment. (PMID: 25070513) Delplanque J … Sablonnière B (Brain : a journal of neurology 2014) 2 3 4 58
  2. A new locus for spinocerebellar ataxia (SCA21) maps to chromosome 7p21.3-p15.1. (PMID: 12402269) Vuillaume I … Sablonnière B (Annals of neurology 2002) 2 3 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4 58
  5. Molecular genetics of hereditary spinocerebellar ataxia: mutation analysis of spinocerebellar ataxia genes and CAG/CTG repeat expansion detection in 225 Italian families. (PMID: 15148151) Brusco A … Taroni F (Archives of neurology 2004) 3 58

Products for TMEM240 Gene

Sources for TMEM240 Gene

Content
Loading form....