UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:CHT1
HGNC Symbol:SLC5A7
HGNC Description:solute carrier family 5 (sodium/choline cotransporter), member 7
HGNC ID:14025
Chromosome:Chr.2(+): 108602979-108630663 GRCh37
OMIM Phenotype:None
Nucleotide RefSeq:NM_021815
Protein RefSeq:NP_068587
Evidence:Substrate In Vitro Evidence: Choline (in oocytes) Uptake is specifically inhibited by hemicholinium 3 Okuda et al 2000, FEBS letters, Vol 484, Issue 2 p. 92-97 Choline (in COS-7 cells (membrane vesicles)) Apparsundaram et al 2000, Biochemical and Biophysical Research Communications, Vol 276, Issue 3, p. 862-867 Choline (in HEK-293 cells, localized primarily to intracellular organelles) Ribeiro et al J Neurochem 2003, Vol 87 (1), p.136-146 Tissue Distribution Evidence: Expressed in tissues containing cholinergic neurons (including spinal cord, medulla, and putamen) by Northern Blot analysis. Okuda et al 2000, FEBS letters, Vol 484, Issue 2 p. 92-97 Apparsundaram et al 2000, Biochemical and Biophysical Research Communications, Vol 276, Issue 3, p. 862-867 Wright and Turk, Pflugers Archives 2003 Expressed in human arterial tissues (RT-PCR) Lips et al 2003, Journal of Histochemistry and Cytochemistry, Vol 51 (12), p.1645-1654 Expressed in keratinocytes and some epithelial tissues (RT-PCR, immunohistochemistry, western blotting) Pfeil et al 2003, Life Sci, Vol 72 (18-19), p.2087-90
Tissues:Spinal cord and medulla (intracellular vesicles)
PharmGKB ID:PA37838
HPRD ID:12294
Trivial Names:CHT, CHT1, hCHT, HMN7A
Transcripts:NM_021815.2 [Chr.2(+): 108602995-108630439 GRCh37]
XM_005264008.1 [Chr.2(+): 108602979-108630663 GRCh37]
XM_005264009.1 [Chr.2(+): 108602980-108630663 GRCh37]
ENST00000264047 [Chr.2(+): 108602995-108630450 GRCh37]
ENST00000409059 [Chr.2(+): 108602979-108627317 GRCh37]
ENST00000540517 [Chr.2(+): 108602980-108627426 GRCh37]
Annotation History:View Events (21)

GTEx Expression by Gene and Transcript

The heat map summarizes relative expression by tissue type at two levels of tissue detail, e.g., 'Brain' and 'Brain - Amygdala'. Choose among four calculated expression values, including mean and median RPKM values, and quantile normalized (QN) distributions of these values. (Note that differences between some distributions are subtle.) The coloring is relative to the mean of all displayed values. All values are log base 2. (See also PMT GTEx Expression Plotting.) Click on a transcript or tissue to resort the data.

Expression values:
No expression data exists for SLC5A7.

Variant Data

View all PMT variants for SLC5A7 on UCSC Genome Browser
Showing SNP features for transcript:   
1000 Genomes  

20141104 phase 3 variant call set of the 20130502 sequence freeze and alignments for SNPs and short indels (indels > 255 and structural variants are not included here). This variant set contains 2504 individuals from 26 populations (mouse over population column heading for population sizes).
Showing gene variants in regions defined by NCBI RefSeq exons, putative promoter, and PMT resequencing assays.
Note: Frequencies are calculated directly from reported genotypes and may vary from consensus frequencies reported by the 1000 Genomes project, which relied on additional data and the GATK tool Variant Quality Score Recalibrator.
dbSNP build 142.
Array availability: I - found on Illumina Human1M-Duo BeadChip (2011-04-21)  A - found on Affymetrix Genome-Wide SNP Array 6.0 (2011-06-21)  
Download the SNP table data as a tab-delimited file.

Transmembrane prediction:

Non-synonymous amino acid changes shown in red, indels (insertions and deletions) in blue, and synonymous changes in green. Exon(s) indicated by black outlines.