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Aliases for TLCD1 Gene

Aliases for TLCD1 Gene

  • TLC Domain Containing 1 2 3 5
  • TLC Domain-Containing Protein 1 3 4
  • Calfacilitin 2 3

External Ids for TLCD1 Gene

Previous GeneCards Identifiers for TLCD1 Gene

  • GC17M024076
  • GC17M027052
  • GC17M023260
  • GC17M027053
  • GC17M027140

Summaries for TLCD1 Gene

GeneCards Summary for TLCD1 Gene

TLCD1 (TLC Domain Containing 1) is a Protein Coding gene. An important paralog of this gene is TLCD2.

UniProtKB/Swiss-Prot for TLCD1 Gene

  • Calcium channel facilitator that increases calcium flux by generating a larger window current and slowing inactivation of the L-type CACNA1C/CaV1.2 channel. Regulation of intracellular calcium by Calfacilitin is required for neural plate formation (By similarity).

Additional gene information for TLCD1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TLCD1 Gene

Genomics for TLCD1 Gene

GeneHancer (GH) Regulatory Elements for TLCD1 Gene

Promoters and enhancers for TLCD1 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
GH17I028715 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 550.4 +5.0 5011 14.4 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000264577 RPL23A RAB34 NEK8 GC17P028741 GC17P028746 GC17P028748 GC17P028753 SNORD42A SNORD4A
GH17I028807 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11 -82.5 -82504 6.8 HDGF PKNOX1 FOXA2 ARNT SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 FAM222B TRAF4 LOC101927018 ERAL1 FLOT2 DHRS13 TLCD1 NEK8 SNORD42A SNORD4B
GH17I028660 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.6 +65.5 65510 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SUPT6H SDF2 PROCA1 ENSG00000264044 SNORD42A SNORD4B SGK494 SPAG5-AS1 NEK8 TLCD1
GH17I028863 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -137.4 -137401 3.3 HDGF SMAD1 ARNT ARID4B IRF4 ZNF766 CBX5 JUNB REST ZNF592 DHRS13 RPL23A PROCA1 NUFIP2 SUPT6H PHF12 ENSG00000264577 ENSG00000265908 FLOT2 TLCD1
GH17I028760 Enhancer 1.1 Ensembl ENCODE dbSUPER 12.2 -33.3 -33336 2.2 ZNF792 PYGO2 ZIC2 THRB RAD21 ETS1 POLR2A SCRT2 RXRA NFIA TRAF4 TLCD1 SNORD42A SNORD4B NEK8 FAM222B ERAL1 SNORD4A SNORD42B RPL23A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TLCD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TLCD1 gene promoter:

Genomic Locations for TLCD1 Gene

Genomic Locations for TLCD1 Gene
chr17:28,724,348-28,727,935
(GRCh38/hg38)
Size:
3,588 bases
Orientation:
Minus strand
chr17:27,051,366-27,054,953
(GRCh37/hg19)

Genomic View for TLCD1 Gene

Genes around TLCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TLCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TLCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TLCD1 Gene

Proteins for TLCD1 Gene

  • Protein details for TLCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96CP7-TLCD1_HUMAN
    Recommended name:
    Calfacilitin
    Protein Accession:
    Q96CP7
    Secondary Accessions:
    • A8MYP9

    Protein attributes for TLCD1 Gene

    Size:
    247 amino acids
    Molecular mass:
    28548 Da
    Quaternary structure:
    • Interacts with CACNA1C.

    Alternative splice isoforms for TLCD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TLCD1 Gene

Post-translational modifications for TLCD1 Gene

No Post-translational modifications

Other Protein References for TLCD1 Gene

No data available for DME Specific Peptides for TLCD1 Gene

Domains & Families for TLCD1 Gene

Gene Families for TLCD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TLCD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TLCD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TLCD1: view

No data available for UniProtKB/Swiss-Prot for TLCD1 Gene

Function for TLCD1 Gene

Molecular function for TLCD1 Gene

UniProtKB/Swiss-Prot Function:
Calcium channel facilitator that increases calcium flux by generating a larger window current and slowing inactivation of the L-type CACNA1C/CaV1.2 channel. Regulation of intracellular calcium by Calfacilitin is required for neural plate formation (By similarity).

Phenotypes From GWAS Catalog for TLCD1 Gene

Phenotypes for TLCD1 Gene

genes like me logo Genes that share phenotypes with TLCD1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for TLCD1 Gene

Localization for TLCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TLCD1 Gene

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 TLCD1 gene
Compartment Confidence
plasma membrane 4
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for TLCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TLCD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TLCD1 Gene

Pathways & Interactions for TLCD1 Gene

SuperPathways for TLCD1 Gene

No Data Available

Interacting Proteins for TLCD1 Gene

Gene Ontology (GO) - Biological Process for TLCD1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for TLCD1 Gene

Drugs & Compounds for TLCD1 Gene

No Compound Related Data Available

Transcripts for TLCD1 Gene

Unigene Clusters for TLCD1 Gene

TLC domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TLCD1 Gene

No ASD Table

Relevant External Links for TLCD1 Gene

GeneLoc Exon Structure for
TLCD1
ECgene alternative splicing isoforms for
TLCD1

Expression for TLCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TLCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TLCD1 Gene

This gene is overexpressed in Heart (31.3) and Breast (24.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TLCD1 Gene



Protein tissue co-expression partners for TLCD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of TLCD1 Gene:

TLCD1

SOURCE GeneReport for Unigene cluster for TLCD1 Gene:

Hs.499952
genes like me logo Genes that share expression patterns with TLCD1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TLCD1 Gene

Orthologs for TLCD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for TLCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TLCD1 33 34
  • 99.87 (n)
dog
(Canis familiaris)
Mammalia TLCD1 33 34
  • 87.61 (n)
cow
(Bos Taurus)
Mammalia TLCD1 33 34
  • 87.46 (n)
mouse
(Mus musculus)
Mammalia Tlcd1 33 16 34
  • 84.76 (n)
rat
(Rattus norvegicus)
Mammalia Tlcd1 33
  • 84.19 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TLCD1 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TLCD1 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves TLCD1 33 34
  • 64.25 (n)
zebrafish
(Danio rerio)
Actinopterygii tlcd1 33 34
  • 51.39 (n)
worm
(Caenorhabditis elegans)
Secernentea Y48G8AL.13 34
  • 18 (a)
ManyToMany
Y63D3A.8 34
  • 18 (a)
ManyToMany
K12H6.6 34
  • 17 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 26 (a)
OneToMany
Species where no ortholog for TLCD1 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)
  • 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 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)

Evolution for TLCD1 Gene

ENSEMBL:
Gene Tree for TLCD1 (if available)
TreeFam:
Gene Tree for TLCD1 (if available)

Paralogs for TLCD1 Gene

Paralogs for TLCD1 Gene

(1) SIMAP similar genes for TLCD1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with TLCD1: view

Variants for TLCD1 Gene

Sequence variations from dbSNP and Humsavar for TLCD1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs759474870 likely-benign, Nephronophthisis 9 28,728,822(-) G/A/T upstream_transcript_variant
rs786204782 uncertain-significance, not specified 28,728,859(-) GGG/GG upstream_transcript_variant
rs1000340537 -- 28,723,984(-) C/G downstream_transcript_variant
rs1001389577 -- 28,729,145(-) G/A upstream_transcript_variant
rs1001630399 -- 28,726,155(-) G/C 5_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TLCD1 Gene

Variant ID Type Subtype PubMed ID
nsv1064087 CNV gain 25217958

Variation tolerance for TLCD1 Gene

Residual Variation Intolerance Score: 35.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TLCD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TLCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TLCD1 Gene

Disorders for TLCD1 Gene

Additional Disease Information for TLCD1

No disorders were found for TLCD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TLCD1 Gene

Publications for TLCD1 Gene

  1. Calfacilitin is a calcium channel modulator essential for initiation of neural plate development. (PMID: 23673622) Papanayotou C … Stern CD (Nature communications 2013) 2 3 58
  2. TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains? (PMID: 12151215) Winter E … Ponting CP (Trends in biochemical sciences 2002) 2 3 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta GD … Pelletier L (Cell 2015) 3 58
  5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 4 58

Products for TLCD1 Gene

Sources for TLCD1 Gene

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