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Aliases for SLC44A4 Gene

Aliases for SLC44A4 Gene

  • Solute Carrier Family 44 Member 4 2 3 4 5
  • Thiamine Pyrophosphate Transporter 1 3 4
  • C6orf29 3 4
  • HTPPT1 3 4
  • CTL4 3 4
  • NG22 3 4
  • Chromosome 6 Open Reading Frame 29 2
  • Solute Carrier Family 44, Member 4 2
  • Choline Transporter-Like Protein 4 3
  • Thiamine Pyrophosphate Transporter 3
  • Testicular Tissue Protein Li 48 3
  • DFNA72 3
  • TPPT1 4
  • TPPT 3

External Ids for SLC44A4 Gene

Previous HGNC Symbols for SLC44A4 Gene

  • C6orf29

Previous GeneCards Identifiers for SLC44A4 Gene

  • GC06M031940
  • GC06M031830
  • GC06M031628

Summaries for SLC44A4 Gene

Entrez Gene Summary for SLC44A4 Gene

  • The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

GeneCards Summary for SLC44A4 Gene

SLC44A4 (Solute Carrier Family 44 Member 4) is a Protein Coding gene. Diseases associated with SLC44A4 include Deafness, Autosomal Dominant 72 and Autosomal Dominant Non-Syndromic Sensorineural Deafness Type Dfna. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Metabolism. An important paralog of this gene is SLC44A2.

UniProtKB/Swiss-Prot for SLC44A4 Gene

  • Choline transporter that plays a role in the choline-acetylcholine system and is required to the efferent innervation of hair cells in the olivocochlear bundle for the maintenance of physiological function of outer hair cells and the protection of hair cells from acoustic injury (By similarity) (PubMed:23651124, PubMed:28013291). Also described as a thiamine pyrophosphate transporter in colon, may mediate the absorption of microbiota-generated thiamine pyrophosphate and contribute to host thiamine (vitamin B1) homeostasis (PubMed:24379411).

  • Isoform 3: Has also thiamine pyrophosphate transporter activity.

Gene Wiki entry for SLC44A4 Gene

Additional gene information for SLC44A4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC44A4 Gene

Genomics for SLC44A4 Gene

GeneHancer (GH) Regulatory Elements for SLC44A4 Gene

Promoters and enhancers for SLC44A4 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
GH06I031876 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 562.7 +0.4 408 4.2 ELF3 PKNOX1 FOXA2 NFIB MLX ARID4B KLF17 BMI1 RAD21 THRB SLC44A4 HLA-DRB5 SKIV2L HLA-DRB1 HLA-C EHMT2 VWA7 DXO HLA-DQA2 C4B
GH06I031538 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.1 +337.9 337907 4.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 DDX39B DDX39B-AS1 GC06M031542 GC06M031962 GC06M031965 GC06M031970 PIR32498 SNORD84 PIR59933 GC06M031573
GH06I032521 Enhancer 1 Ensembl dbSUPER 10.1 -642.9 -642855 0.2 ZSCAN4 GLI4 ZNF2 ZNF335 ZNF302 ZNF366 SP3 ZNF398 ELF1 ZEB2 GC06M032524 HLA-DRB1 HLA-DRB6 HLA-DQA2 HLA-DRB5 LSM2 BRD2 DDX39B ATF6B DAXX
GH06I031910 Enhancer 1 Ensembl ENCODE 8.2 -32.1 -32132 2 INSM2 KLF17 BATF RFX5 GTF3C2 ZNF335 EGR1 ZNF366 FOS SMARCA5 C4A SKIV2L HLA-DRB5 HLA-C MICB MIR1236 NEU1 STK19 GPANK1 LY6G5B
GH06I031486 Enhancer 0.2 Ensembl 4.5 +392.8 392845 0.4 GC06M031422 PPIAP9 RPL15P4 MCCD1 SNORD117 DDX39B ATP6V1G2 DDX39B-AS1 SLC44A4 MICB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC44A4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC44A4 gene promoter:

Genomic Locations for SLC44A4 Gene

Genomic Locations for SLC44A4 Gene
chr6:31,863,192-31,879,046
(GRCh38/hg38)
Size:
15,855 bases
Orientation:
Minus strand
chr6:31,830,969-31,846,823
(GRCh37/hg19)

Genomic View for SLC44A4 Gene

Genes around SLC44A4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC44A4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC44A4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for SLC44A4 Gene

  • Protein details for SLC44A4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q53GD3-CTL4_HUMAN
    Recommended name:
    Choline transporter-like protein 4
    Protein Accession:
    Q53GD3
    Secondary Accessions:
    • A2BED3
    • B0UXX8
    • B0UZY8
    • B4DU94
    • B4DWM2
    • E9PEK7
    • Q5JP84
    • Q5JQ93
    • Q658S8
    • Q6UX89
    • Q8TEW4
    • Q96C58
    • Q96K59
    • Q9Y332

    Protein attributes for SLC44A4 Gene

    Size:
    710 amino acids
    Molecular mass:
    79254 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC44A4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC44A4 Gene

Post-translational modifications for SLC44A4 Gene

  • N-glycosylated; N-glycosylation of Asn-69, Asn-155 and Asn-393 is required for a proper thiamine pyrophosphate uptake.
  • Glycosylation at isoforms=469, isoforms=3155, isoforms=3, 4197, posLast=298298, posLast=393393, posLast=405405, and posLast=416416

Other Protein References for SLC44A4 Gene

No data available for DME Specific Peptides for SLC44A4 Gene

Domains & Families for SLC44A4 Gene

Gene Families for SLC44A4 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC44A4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q53GD3

UniProtKB/Swiss-Prot:

CTL4_HUMAN :
  • Belongs to the CTL (choline transporter-like) family.
Family:
  • Belongs to the CTL (choline transporter-like) family.
genes like me logo Genes that share domains with SLC44A4: view

Function for SLC44A4 Gene

Molecular function for SLC44A4 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.17 uM for thiamine pyrophosphate {ECO:0000269 PubMed:24379411}; Vmax=18.19 pmol/min/mg enzyme {ECO:0000269 PubMed:24379411};
UniProtKB/Swiss-Prot Function:
Choline transporter that plays a role in the choline-acetylcholine system and is required to the efferent innervation of hair cells in the olivocochlear bundle for the maintenance of physiological function of outer hair cells and the protection of hair cells from acoustic injury (By similarity) (PubMed:23651124, PubMed:28013291). Also described as a thiamine pyrophosphate transporter in colon, may mediate the absorption of microbiota-generated thiamine pyrophosphate and contribute to host thiamine (vitamin B1) homeostasis (PubMed:24379411).
UniProtKB/Swiss-Prot Function:
Isoform 3: Has also thiamine pyrophosphate transporter activity.

Phenotypes From GWAS Catalog for SLC44A4 Gene

Gene Ontology (GO) - Molecular Function for SLC44A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015220 choline transmembrane transporter activity TAS --
GO:0090422 thiamine pyrophosphate transmembrane transporter activity IMP 24379411
genes like me logo Genes that share ontologies with SLC44A4: view
genes like me logo Genes that share phenotypes with SLC44A4: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC44A4 Gene

Localization for SLC44A4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC44A4 Gene

Membrane; Multi-pass membrane protein. Apical cell membrane.

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 SLC44A4 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for SLC44A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IDA,IEA 24379411
GO:0070062 extracellular exosome HDA,IDA 19056867
genes like me logo Genes that share ontologies with SLC44A4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC44A4 Gene

Pathways & Interactions for SLC44A4 Gene

genes like me logo Genes that share pathways with SLC44A4: view

Pathways by source for SLC44A4 Gene

Interacting Proteins for SLC44A4 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000229729%0d%0a9606.ENSP00000355173%0d%0a
Selected Interacting proteins: ENSP00000229729 Q53GD3-CTL4_HUMAN for SLC44A4 Gene via STRING IID

Gene Ontology (GO) - Biological Process for SLC44A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0008292 acetylcholine biosynthetic process IMP 23651124
GO:0015871 choline transport IMP 23651124
GO:0030307 positive regulation of cell growth IMP 23651124
GO:0030974 thiamine pyrophosphate transmembrane transport IMP 24379411
genes like me logo Genes that share ontologies with SLC44A4: view

No data available for SIGNOR curated interactions for SLC44A4 Gene

Drugs & Compounds for SLC44A4 Gene

(1) Drugs for SLC44A4 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Transporter, substrate 176
genes like me logo Genes that share compounds with SLC44A4: view

Transcripts for SLC44A4 Gene

Unigene Clusters for SLC44A4 Gene

Solute carrier family 44, member 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC44A4 Gene

No ASD Table

Relevant External Links for SLC44A4 Gene

GeneLoc Exon Structure for
SLC44A4
ECgene alternative splicing isoforms for
SLC44A4

Expression for SLC44A4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC44A4 Gene

mRNA differential expression in normal tissues according to GTEx for SLC44A4 Gene

This gene is overexpressed in Colon - Transverse (x16.4), Stomach (x6.7), Prostate (x6.4), and Small Intestine - Terminal Ileum (x5.4).

Protein differential expression in normal tissues from HIPED for SLC44A4 Gene

This gene is overexpressed in Urine (56.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLC44A4 Gene



Protein tissue co-expression partners for SLC44A4 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC44A4 Gene:

SLC44A4

SOURCE GeneReport for Unigene cluster for SLC44A4 Gene:

Hs.335355

mRNA Expression by UniProt/SwissProt for SLC44A4 Gene:

Q53GD3-CTL4_HUMAN
Tissue specificity: Highly expressed in colon, also detected in prostate, trachea and lung (PubMed:24379411). Isoform 3 is also expressed in colon but a lower levels (PubMed:24379411).

Evidence on tissue expression from TISSUES for SLC44A4 Gene

  • Intestine(4.8)
  • Stomach(4.2)
  • Pancreas(3.7)
genes like me logo Genes that share expression patterns with SLC44A4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC44A4 Gene

Orthologs for SLC44A4 Gene

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

Orthologs for SLC44A4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC44A4 33 34
  • 99.01 (n)
dog
(Canis familiaris)
Mammalia SLC44A4 33 34
  • 87.19 (n)
cow
(Bos Taurus)
Mammalia SLC44A4 33 34
  • 85.1 (n)
rat
(Rattus norvegicus)
Mammalia Slc44a4 33
  • 81.82 (n)
mouse
(Mus musculus)
Mammalia Slc44a4 33 16 34
  • 81.49 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC44A4 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC44A4 34
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC44A4 34
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc44a4 33
  • 62.44 (n)
zebrafish
(Danio rerio)
Actinopterygii slc44a4 33
  • 62.72 (n)
SLC44A4 34
  • 48 (a)
OneToOne
zgc64108 33
fruit fly
(Drosophila melanogaster)
Insecta CG11880 33 34
  • 51.29 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta CTLH2_ANOGA 33
  • 47.98 (n)
worm
(Caenorhabditis elegans)
Secernentea chtl-1 34
  • 36 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PNS1 34
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToMany
Species where no ortholog for SLC44A4 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)
  • 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)
  • 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)

Evolution for SLC44A4 Gene

ENSEMBL:
Gene Tree for SLC44A4 (if available)
TreeFam:
Gene Tree for SLC44A4 (if available)

Paralogs for SLC44A4 Gene

Paralogs for SLC44A4 Gene

(2) SIMAP similar genes for SLC44A4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLC44A4: view

Variants for SLC44A4 Gene

Sequence variations from dbSNP and Humsavar for SLC44A4 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs104893986 pathogenic, Sialidosis, type II 31,862,708(-) C/T downstream_transcript_variant
rs374172739 uncertain-significance, Sialidosis, type II 31,862,825(-) G/A downstream_transcript_variant
rs41267082 likely-benign, Sialidosis, type II 31,862,816(-) A/C/G/T downstream_transcript_variant
rs563426936 A colorectal cancer sample 31,869,156(-) G/A coding_sequence_variant, missense_variant
rs566696697 uncertain-significance, Sialidosis, type II 31,862,852(-) G/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC44A4 Gene

Variant ID Type Subtype PubMed ID
nsv601960 CNV loss 21841781
nsv509126 CNV insertion 20534489
nsv508399 CNV deletion 20534489
nsv1126749 CNV deletion 24896259
nsv1112900 CNV deletion 24896259
nsv1073969 CNV deletion 25765185
dgv10463n54 CNV loss 21841781
dgv10461n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
dgv10403n54 CNV loss 21841781

Variation tolerance for SLC44A4 Gene

Residual Variation Intolerance Score: 67.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.97; 68.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC44A4 Gene

Human Gene Mutation Database (HGMD)
SLC44A4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC44A4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC44A4 Gene

Disorders for SLC44A4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SLC44A4 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal dominant 72
  • dfna72
autosomal dominant non-syndromic sensorineural deafness type dfna
  • autosomal dominant isolated neurosensory deafness type dfna
endocervical carcinoma
  • carcinoma of endocervix
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CTL4_HUMAN
  • Deafness, autosomal dominant, 72 (DFNA72) [MIM:617606]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA72 primarily affects the middle frequencies. It gradually progresses to whole-frequency hearing loss. {ECO:0000269 PubMed:28013291}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=An interstitial deletion causing the fusion of exon 10 of CTL4 with the 3-UTR of NEU has been detected in two patients affected by sialidosis.

Additional Disease Information for SLC44A4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC44A4: view

No data available for Genatlas for SLC44A4 Gene

Publications for SLC44A4 Gene

  1. SLC44A4 mutation causes autosomal dominant hereditary postlingual non-syndromic mid-frequency hearing loss. (PMID: 28013291) Ma Z … Ma D (Human molecular genetics 2017) 2 3 4 58
  2. Molecular identification and functional characterization of the human colonic thiamine pyrophosphate transporter. (PMID: 24379411) Nabokina SM … Said HM (The Journal of biological chemistry 2014) 2 3 4 58
  3. An electric lobe suppressor for a yeast choline transport mutation belongs to a new family of transporter-like proteins. (PMID: 10677542) O'Regan S … Meunier FM (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 58
  4. Identification of critical variants within SLC44A4, an ulcerative colitis susceptibility gene identified in a GWAS in north Indians. (PMID: 26741288) Gupta A … Thelma BK (Genes and immunity 2016) 3 4 58
  5. The human colonic thiamine pyrophosphate transporter (hTPPT) is a glycoprotein and N-linked glycosylation is important for its function. (PMID: 26828122) Nabokina SM … Said HM (Biochimica et biophysica acta 2016) 3 4 58

Products for SLC44A4 Gene

Sources for SLC44A4 Gene

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