Aliases for SLC44A2 Gene

Aliases for SLC44A2 Gene

  • Solute Carrier Family 44 Member 2 2 3 4 5
  • CTL2 2 3 4
  • Solute Carrier Family 44 (Choline Transporter), Member 2 2 3
  • Choline Transporter-Like Protein 2 3 4
  • Testicular Tissue Protein Li 47 3
  • SLC44A2 5
  • PP1292 3

External Ids for SLC44A2 Gene

Previous GeneCards Identifiers for SLC44A2 Gene

  • GC19P010575
  • GC19P010713
  • GC19P010290

Summaries for SLC44A2 Gene

GeneCards Summary for SLC44A2 Gene

SLC44A2 (Solute Carrier Family 44 Member 2) is a Protein Coding gene. Diseases associated with SLC44A2 include Femoral Vein Thrombophlebitis and Deafness, Autosomal Recessive 68. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Innate Immune System. Gene Ontology (GO) annotations related to this gene include obsolete signal transducer activity and choline transmembrane transporter activity. An important paralog of this gene is SLC44A5.

UniProtKB/Swiss-Prot Summary for SLC44A2 Gene

  • Isoform 1, but not isoform 3, exhibits some choline transporter activity.

Gene Wiki entry for SLC44A2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC44A2 Gene

Genomics for SLC44A2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC44A2 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
GH19J010601 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 284.3 +1.5 1502 4.7 ZBTB10 MNT IKZF1 ZNF217 ELF1 ZIC2 ZNF610 SIN3B VEZF1 SAP130 SLC44A2 CDKN2D KRI1 ICAM3 ILF3 TYK2 DNM2 S1PR5 ATG4D AP1M2
GH19J010624 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 274.6 +23.3 23319 2.9 ZBTB10 ZNF217 ZBTB7B ELF1 ZIC2 SIN3A REST KLF9 YY1 SP2 SLC44A2 ELOF1 ILF3-DT DNMT1 RF00017-2807 HSALNG0123949 ILF3 lnc-TIMM29-1
GH19J010717 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 18.2 +116.4 116419 4.3 CHD2 TBP MXD4 SP1 FEZF1 CEBPA SIX5 NR2C1 MNT DEK DNM2 MIR638 ILF3 KRI1 EIF3G ZNF627 FBXL12 PPAN RAVER1 UBE2L4
GH19J010651 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 17.6 +51.9 51873 5.3 TBP ZBTB10 BCL11A MXD4 SP1 FEZF1 CEBPA SIX5 NR2C1 MNT ILF3 ILF3-DT piR-46435 piR-61384 ZNF627 LOC100419831 KRI1 DNMT1 FBXL12 RAVER1
GH19J010746 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 22 +147.6 147623 6.5 MXD4 MNT IKZF1 ZFP64 BHLHE40 ZEB1 ZIC2 THAP11 ARNT RAD51 SLC44A2 KRI1 RAVER1 ZNF627 ILF3 FBXL12 DNMT1 LOC100419831 PRKCSH PPAN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC44A2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC44A2

Top Transcription factor binding sites by QIAGEN in the SLC44A2 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • Ik-2
  • NF-Y
  • NF-YA
  • Sp1
  • USF-1
  • USF1

Genomic Locations for SLC44A2 Gene

Latest Assembly
42,103 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
42,103 bases
Plus strand

(GRCh37/hg19 by Ensembl)
42,103 bases
Plus strand

Genomic View for SLC44A2 Gene

Genes around SLC44A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC44A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC44A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC44A2 Gene

Proteins for SLC44A2 Gene

  • Protein details for SLC44A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Choline transporter-like protein 2
    Protein Accession:
    Secondary Accessions:
    • B2RBB1
    • B3KNH3
    • B4DFJ0
    • F2Q9D7
    • Q658V1
    • Q658Z2
    • Q6PJV7
    • Q8N2F0
    • Q9NY68

    Protein attributes for SLC44A2 Gene

    706 amino acids
    Molecular mass:
    80124 Da
    Quaternary structure:
    • Interacts with COCH.
    • Sequence=BAC11662.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
    • [Isoform 3]: Produced by alternative promoter usage.

    Alternative splice isoforms for SLC44A2 Gene


neXtProt entry for SLC44A2 Gene

Post-translational modifications for SLC44A2 Gene

  • Glycosylation at Asn187, Asn200, and Asn417
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for SLC44A2 Gene

Domains & Families for SLC44A2 Gene

Gene Families for SLC44A2 Gene

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

Protein Domains for SLC44A2 Gene


Suggested Antigen Peptide Sequences for SLC44A2 Gene

GenScript: Design optimal peptide antigens:
  • Solute carrier family 44 member 2 (CTL2_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the CTL (choline transporter-like) family.
  • Belongs to the CTL (choline transporter-like) family.
genes like me logo Genes that share domains with SLC44A2: view

Function for SLC44A2 Gene

Molecular function for SLC44A2 Gene

UniProtKB/Swiss-Prot Function:
Isoform 1, but not isoform 3, exhibits some choline transporter activity.

Phenotypes From GWAS Catalog for SLC44A2 Gene

Gene Ontology (GO) - Molecular Function for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015220 choline transmembrane transporter activity IBA,TAS 10677542
GO:0022857 transmembrane transporter activity IEA,IBA 21873635
genes like me logo Genes that share ontologies with SLC44A2: view
genes like me logo Genes that share phenotypes with SLC44A2: view

Animal Models for SLC44A2 Gene

MGI Knock Outs for SLC44A2:

Animal Models for research

  • Taconic Biosciences Mouse Models for SLC44A2

miRNA for SLC44A2 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC44A2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC44A2 Gene

Localization for SLC44A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC44A2 Gene

Membrane. Multi-pass membrane protein.

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 SLC44A2 gene
Compartment Confidence
plasma membrane 5
extracellular 4
mitochondrion 4
lysosome 4
cytoskeleton 3
peroxisome 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 26746385
GO:0005765 lysosomal membrane HDA 17897319
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA,IBA 21873635
GO:0016021 integral component of membrane IEA,TAS 10677542
genes like me logo Genes that share ontologies with SLC44A2: view

Pathways & Interactions for SLC44A2 Gene

genes like me logo Genes that share pathways with SLC44A2: view

Pathways by source for SLC44A2 Gene

Interacting Proteins for SLC44A2 Gene

SIGNOR curated interactions for SLC44A2 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0015871 choline transport TAS 10677542
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling HMP 12761501
GO:0043312 neutrophil degranulation TAS --
GO:0055085 transmembrane transport IEA,TAS --
genes like me logo Genes that share ontologies with SLC44A2: view

Drugs & Compounds for SLC44A2 Gene

(1) Drugs for SLC44A2 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Transporter, substrate 235
genes like me logo Genes that share compounds with SLC44A2: view

Transcripts for SLC44A2 Gene

mRNA/cDNA for SLC44A2 Gene

22 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC44A2

Alternative Splicing Database (ASD) splice patterns (SP) for SLC44A2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b · 14c ^ 15a · 15b ^ 16a · 16b · 16c ·
SP1: - - -
SP2: - - - - -
SP3: - - -
SP4: - - -
SP7: - - - - - - - - - - - - - - - - - - -
SP9: -
SP10: -

ExUns: 16d · 16e ^ 17a · 17b · 17c ^ 18a · 18b · 18c ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b
SP1: - -
SP2: - -
SP3: - - - -
SP6: -

Relevant External Links for SLC44A2 Gene

GeneLoc Exon Structure for

Expression for SLC44A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC44A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC44A2 Gene

This gene is overexpressed in Whole Blood (x4.8).

Protein differential expression in normal tissues from HIPED for SLC44A2 Gene

This gene is overexpressed in Nasal epithelium (43.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC44A2 Gene

Protein tissue co-expression partners for SLC44A2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC44A2

SOURCE GeneReport for Unigene cluster for SLC44A2 Gene:


mRNA Expression by UniProt/SwissProt for SLC44A2 Gene:

Tissue specificity: Present in supporting cells of the inner ear (at protein level). Only isoform 3 is expressed in inner ear vestibular tissue.

Evidence on tissue expression from TISSUES for SLC44A2 Gene

  • Nervous system(5)
  • Stomach(4.5)
  • Liver(4.4)
  • Eye(4.4)
  • Lung(4.4)
  • Kidney(3.4)
  • Intestine(3)
  • Muscle(2.9)
  • Skin(2.6)
  • Heart(2.5)
  • Spleen(2.5)
  • Blood(2.4)
  • Lymph node(2.2)
genes like me logo Genes that share expression patterns with SLC44A2: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC44A2 Gene

Orthologs for SLC44A2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SLC44A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC44A2 30 31
  • 99.76 (n)
(Canis familiaris)
Mammalia SLC44A2 30 31
  • 89.73 (n)
(Bos Taurus)
Mammalia SLC44A2 30 31
  • 87.77 (n)
(Monodelphis domestica)
Mammalia SLC44A2 31
  • 85 (a)
(Rattus norvegicus)
Mammalia Slc44a2 30
  • 84.95 (n)
(Mus musculus)
Mammalia Slc44a2 30 17 31
  • 84.78 (n)
(Ornithorhynchus anatinus)
Mammalia SLC44A2 31
  • 56 (a)
(Gallus gallus)
Aves SLC44A2 31
  • 72 (a)
(Anolis carolinensis)
Reptilia SLC44A2 31
  • 80 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slc44a2 30
  • 72.68 (n)
Str.7588 30
(Danio rerio)
Actinopterygii slc44a2 30 31
  • 69.24 (n)
SLC44A2 (1 of 2) 31
  • 63 (a)
sbcb39 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10852 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG11880 31
  • 31 (a)
(Caenorhabditis elegans)
Secernentea chtl-1 31
  • 35 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PNS1 31
  • 19 (a)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G15380 30
  • 42.49 (n)
(Oryza sativa)
Liliopsida Os04g0681600 30
  • 43.59 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.12838 30
Species where no ortholog for SLC44A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SLC44A2 Gene

Gene Tree for SLC44A2 (if available)
Gene Tree for SLC44A2 (if available)
Evolutionary constrained regions (ECRs) for SLC44A2: view image

Paralogs for SLC44A2 Gene

Paralogs for SLC44A2 Gene

(4) SIMAP similar genes for SLC44A2 Gene using alignment to 8 proteins:

  • K7ER17_HUMAN
genes like me logo Genes that share paralogs with SLC44A2: view

Variants for SLC44A2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC44A2 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs35362308 Benign: not provided 10,635,053(+) A/G
NM_020428.4(SLC44A2):c.1035A>G (p.Ala345=)
rs7255431 Benign: not provided 10,635,247(+) C/T
NM_020428.4(SLC44A2):c.1140C>T (p.Ser380=)
rs2288904 - p.Gln154Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SLC44A2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SLC44A2 Gene

Variant ID Type Subtype PubMed ID
nsv1071907 CNV deletion 25765185
nsv1127651 CNV deletion 24896259
nsv1160584 CNV deletion 26073780
nsv833744 CNV loss 17160897
nsv833745 CNV loss 17160897

Variation tolerance for SLC44A2 Gene

Residual Variation Intolerance Score: 20% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.44; 42.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC44A2 Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC44A2 Gene

Disorders for SLC44A2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SLC44A2 Gene - From: COP

Disorder Aliases PubMed IDs
femoral vein thrombophlebitis
  • phlebitis and thrombophlebitis of femoral vein
deafness, autosomal recessive 68
  • dfnb68
choline deficiency disease
  • choline deficiency
  • infection by toxascaris
coffin-siris syndrome 1
  • css1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC44A2

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SLC44A2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC44A2 Gene

Publications for SLC44A2 Gene

  1. Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear. (PMID: 17926100) Kommareddi PK … Carey TE (Journal of the Association for Research in Otolaryngology : JARO 2007) 3 4 23
  2. Identification and characterization of choline transporter-like protein 2, an inner ear glycoprotein of 68 and 72 kDa that is the target of antibody-induced hearing loss. (PMID: 14973250) Nair TS … Carey TE (The Journal of neuroscience : the official journal of the Society for Neuroscience 2004) 3 4 23
  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
  4. Isoforms, expression, glycosylation, and tissue distribution of CTL2/SLC44A2. (PMID: 20665236) Kommareddi PK … Carey TE (The protein journal 2010) 3 4
  5. The neutrophil alloantigen HNA-3a (5b) is located on choline transporter-like protein 2 and appears to be encoded by an R>Q154 amino acid substitution. (PMID: 20040764) Curtis BR … Aster RH (Blood 2010) 3 23

Products for SLC44A2 Gene

Sources for SLC44A2 Gene