|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC5A6 |
Basic gene info. | Gene symbol | SLC5A6 |
Gene name | solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6 | |
Synonyms | SMVT | |
Cytomap | UCSC genome browser: 2p23 | |
Genomic location | chr2 :27422454-27435175 | |
Type of gene | protein-coding | |
RefGenes | NM_021095.2, NR_028323.1, | |
Ensembl id | ENSG00000138074 | |
Description | Na(+)-dependent multivitamin transporterNa+-dependent multivitamin transportersodium-dependent multivitamin transportersolute carrier family 5 (sodium-dependent vitamin transporter), member 6solute carrier family 5 member 6 | |
Modification date | 20141211 | |
dbXrefs | MIM : 604024 | |
HGNC : HGNC | ||
Ensembl : ENSG00000138074 | ||
HPRD : 04934 | ||
Vega : OTTHUMG00000097075 | ||
Protein | UniProt: Q9Y289 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SLC5A6 | |
BioGPS: 8884 | ||
Gene Expression Atlas: ENSG00000138074 | ||
The Human Protein Atlas: ENSG00000138074 | ||
Pathway | NCI Pathway Interaction Database: SLC5A6 | |
KEGG: SLC5A6 | ||
REACTOME: SLC5A6 | ||
ConsensusPathDB | ||
Pathway Commons: SLC5A6 | ||
Metabolism | MetaCyc: SLC5A6 | |
HUMANCyc: SLC5A6 | ||
Regulation | Ensembl's Regulation: ENSG00000138074 | |
miRBase: chr2 :27,422,454-27,435,175 | ||
TargetScan: NM_021095 | ||
cisRED: ENSG00000138074 | ||
Context | iHOP: SLC5A6 | |
cancer metabolism search in PubMed: SLC5A6 | ||
UCL Cancer Institute: SLC5A6 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
Top |
Phenotypic Information for SLC5A6(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: SLC5A6 |
Familial Cancer Database: SLC5A6 |
* This gene is included in those cancer gene databases. |
. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
![]() | |
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS |
![]() | |
OMIM | 604024; gene. |
Orphanet | |
Disease | KEGG Disease: SLC5A6 |
MedGen: SLC5A6 (Human Medical Genetics with Condition) | |
ClinVar: SLC5A6 | |
Phenotype | MGI: SLC5A6 (International Mouse Phenotyping Consortium) |
PhenomicDB: SLC5A6 |
Mutations for SLC5A6 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
![]() |
There's no structural variation information in COSMIC data for this gene. |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC5A6 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BQ022479 | RAB11B | 15 | 179 | 19 | 8469049 | 8469213 | SLC5A6 | 174 | 300 | 2 | 27423959 | 27424321 |
![]() |
Top |
![]() |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=49) | (# total SNVs=19) |
![]() | ![]() |
(# total SNVs=1) | (# total SNVs=0) |
![]() |
Top |
![]() |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr2:27426127-27426127 | p.R394L | 4 |
chr2:27424662-27424662 | p.I472I | 3 |
chr2:27423438-27423438 | p.D592N | 3 |
chr2:27425742-27425742 | p.G405D | 2 |
chr2:27430161-27430161 | p.V120I | 2 |
chr2:27427751-27427751 | p.F261F | 2 |
chr2:27426157-27426157 | p.R384Q | 2 |
chr2:27427384-27427384 | p.A317V | 2 |
chr2:27423930-27423930 | p.P567L | 2 |
chr2:27427798-27427798 | p.L246M | 2 |
Top |
![]() |
|
![]() |
Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 4 |   | 9 | 1 |   | 1 |   | 3 | 2 |   | 6 | 5 | 3 |   |   | 12 | 14 | 1 | 6 |
# mutation | 1 | 4 |   | 10 | 1 |   | 1 |   | 3 | 2 |   | 7 | 5 | 3 |   |   | 13 | 14 | 1 | 7 |
nonsynonymous SNV | 1 | 3 |   | 8 | 1 |   | 1 |   | 2 | 2 |   | 6 | 2 | 3 |   |   | 4 | 8 |   | 4 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   | 1 |   |   | 1 | 3 |   |   |   | 9 | 6 | 1 | 3 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
Top |
![]() |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr2:27423930 | p.P567Q | 2 |
chr2:27429797 | p.R384L | 2 |
chr2:27427751 | p.F261F | 2 |
chr2:27427384 | p.A317V | 2 |
chr2:27423438 | p.D592N | 2 |
chr2:27426157 | p.R136Q | 2 |
chr2:27427677 | p.M397V | 1 |
chr2:27423917 | p.L282L | 1 |
chr2:27429763 | p.T127S | 1 |
chr2:27424857 | p.P567P | 1 |
![]() |
![]() |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
![]() |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
Top |
Gene Expression for SLC5A6 |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
![]() |
Top |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
![]() | |||||
ATL2,CAD,CEACAM19,CENPA,DNAJC2,FAM136A,FAM171A1, GPN1,GTF3C2,GTPBP4,KCMF1,MEMO1,NOL10,NOP2, PDSS1,PPM1G,RNASEH1,SLC5A6,TCF7L1,TTLL4,WDR43 | APOBEC3B,C11orf16,KIAA1549L,CHI3L2,DAPP1,GABRP,GINS4, LTF,MCM2,MEX3A,MMP7,ORC1,PROM1,RCC2, SLC34A2,SLC5A6,SMARCD1,TGIF2,TMEM158,TP53,TTLL4 | ||||
![]() | |||||
ATIC,AAR2,CIAO1,EIF2S2,ERGIC3,LDLRAD3,NCK2, PIGU,PLAGL2,PNPT1,POFUT1,RALY,RNF43,SLC19A3, SLC2A8,SLC5A6,SMYD5,TAF4,TP53RK,VIL1,ZNRF3 | ALG3,ANKEF1,ATAD3A,CDC25A,DARS2,EFTUD2,EPHA1, FARSA,FGFR4,HSPA9,HSPD1,MYO19,NCLN,NOP14, NSUN2,PGD,PUS1,SEC61A1,SLC5A6,VARS,WDR4 |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
Top |
![]() |
Top |
Pharmacological Information for SLC5A6 |
![]() |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA379; -. |
Organism-specific databases | CTD | 8884; -. |
![]() |
* Gene Centered Interaction Network. |
![]() |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00121 | solute carrier family 5 (sodium-dependent vitamin transporter), member 6 | approved; nutraceutical | Biotin | ![]() | ![]() |
DB00166 | solute carrier family 5 (sodium-dependent vitamin transporter), member 6 | approved; nutraceutical | Lipoic Acid | ![]() | ![]() |
Top |
Cross referenced IDs for SLC5A6 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |