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mutLBSgeneDB |
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| Gene summary for NR1H4 |
 Gene summary |
| Basic gene Info. | Gene symbol | NR1H4 |
| Gene name | nuclear receptor subfamily 1, group H, member 4 | |
| Synonyms | BAR|FXR|HRR-1|HRR1|RIP14 | |
| Cytomap | UCSC genome browser: 12q23.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001206977.1, NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1, NM_005123.3, | |
| Description | RXR-interacting protein 14bile acid receptorfarnesoid X nuclear receptorfarnesoid X-activated receptorfarnesol receptor HRR-1retinoid X receptor-interacting protein 14 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 603826 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000012504 | ||
| HPRD : 04827 | ||
| Vega : OTTHUMG00000170359 | ||
| Protein | UniProt: Q96RI1 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NR1H4 | |
| BioGPS: 9971 | ||
| Pathway | NCI Pathway Interaction Database: NR1H4 | |
| KEGG: NR1H4 | ||
| REACTOME: NR1H4 | ||
| Pathway Commons: NR1H4 | ||
| Context | iHOP: NR1H4 | |
| ligand binding site mutation search in PubMed: NR1H4 | ||
| UCL Cancer Institute: NR1H4 | ||
| Assigned class in mutLBSgeneDB | A: This gene has a literature evidence and it belongs to targetable_mutLBSgenes. | |
| References showing study about ligand binding site mutation for NR1H4. | 1. Gineste, R., Sirvent, A., Paumelle, R., Helleboid, S., Aquilina, A., Darteil, R., ... & Staels, B. (2008). Phosphorylation of farnesoid X receptor by protein kinase C promotes its transcriptional activity. Molecular Endocrinology,22(11), 2433-2447. 18755856 | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0038185 | intracellular bile acid receptor signaling pathway | 10334992 | GO:0070858 | negative regulation of bile acid biosynthetic process | 10334992 |
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| Ligand binding site mutations for NR1H4 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | A462 | D462Y | COAD | 1 | G357 | R357Q | COAD | 1 | E328 | A328G | LUAD | 1 | K286 | E286Q | LUSC | 1 | W468,M466 | P467T | LUSC | 1 | E291 | T292M | OV | 1 | K335 | A337V | SKCM | 1 | K317 | D316N | SKCM | 1 | M304 | E304D | STAD | 1 | K335 | R335H | UCEC | 1 | E290 | I290M | UCEC | 1 | I287 | F288V | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, 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. |
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| Protein structure related information for NR1H4 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for NR1H4 from PDB |
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| Differential gene expression and gene-gene network for NR1H4 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for NR1H4 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0008370 | Cholestasis | 8 | AlteredExpression, Biomarker |
| umls:C0023903 | Liver Neoplasms | 6 | Biomarker |
| umls:C2239176 | Carcinoma, Hepatocellular | 5 | Biomarker |
| umls:C0023895 | Liver Diseases | 5 | Biomarker, GeneticVariation |
| umls:C0010346 | Crohn Disease | 3 | Biomarker |
| umls:C0860207 | Drug-Induced Liver Injury | 1 | Biomarker |
| umls:C0015379 | Extravasation of Diagnostic and Therapeutic Materials | 1 | Biomarker |
| umls:C0021841 | Intestinal Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for NR1H4 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB02545 | Fexaramine | Small molecule |  |
| Approved | DB06777 | Chenodeoxycholic acid | Small molecule |  |
| Experimental | DB08220 | (8alpha,10alpha,13alpha,17beta)-17-[(4-hydroxyphenyl)carbonyl]androsta-3,5-diene-3-carboxylic acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of NR1H4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of NR1H4 |
| Multiple alignments for Q96RI1 in multiple species |
| LBS | AA sequence | # species | Species | A305 | ILTEMATSHVQ | 3 | Bos taurus, Mus musculus, Rattus norvegicus | A305 | ILTEMATNHVQ | 1 | Homo sapiens | A462 | FNHHHAEMLMS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A462 | FNHHHADMLMS | 1 | Bos taurus | D484 | LCEIWDVQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E290 | NKILKEEFSAE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E290 | NKFLKEEFSAE | 1 | Bos taurus | E291 | KILKEEFSAEE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E291 | KFLKEEFSAEE | 1 | Bos taurus | E314 | VQVLVEFTKKL | 2 | Homo sapiens, Bos taurus | E314 | VQILVEFTKKL | 1 | Mus musculus | E314 | VQILVEFTKRL | 1 | Rattus norvegicus | E328 | QTLDHEDQIAL | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E481 | TPLLCEIWDVQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F298 | SAEENFLILTE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F298 | SAEENFIILTE | 1 | Bos taurus | F322 | KKLPGFQTLDH | 3 | Homo sapiens, Bos taurus, Mus musculus | F322 | KRLPGFQTLDH | 1 | Rattus norvegicus | F343 | AVEAMFLRSAE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F350 | RSAEIFNKKLP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F350 | RSAEIFSKKLP | 1 | Bos taurus | F380 | YITPMFSFYKS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F475 | VNDHKFTPLLC | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G357 | KKLPAGHADLL | 2 | Mus musculus, Rattus norvegicus | G357 | KKLPSGHSDLL | 1 | Homo sapiens | G357 | KKLPAGHTDLL | 1 | Bos taurus | H308 | EMATSHVQILV | 2 | Mus musculus, Rattus norvegicus | H308 | EMATNHVQVLV | 1 | Homo sapiens | H308 | EMATSHVQVLV | 1 | Bos taurus | H327 | FQTLDHEDQIA | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | H358 | KLPAGHADLLE | 2 | Mus musculus, Rattus norvegicus | H358 | KLPSGHSDLLE | 1 | Homo sapiens | H358 | KLPAGHTDLLE | 1 | Bos taurus | H461 | TFNHHHAEMLM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H461 | TFNHHHADMLM | 1 | Bos taurus | I283 | RMPQEITNKIL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I283 | RMPQEITNKFL | 1 | Bos taurus | I287 | EITNKILKEEF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I287 | EITNKFLKEEF | 1 | Bos taurus | I300 | EENFLILTEMA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I300 | EENFIILTEMA | 1 | Bos taurus | I331 | DHEDQIALLKG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | I349 | LRSAEIFNKKL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I349 | LRSAEIFSKKL | 1 | Bos taurus | I366 | LLEERIRKSGI | 3 | Bos taurus, Mus musculus, Rattus norvegicus | I366 | LLEERIRNSGI | 1 | Homo sapiens | I371 | IRKSGISDEYI | 3 | Bos taurus, Mus musculus, Rattus norvegicus | I371 | IRNSGISDEYI | 1 | Homo sapiens | I376 | ISDEYITPMFS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | I482 | PLLCEIWDVQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K286 | QEITNKILKEE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K286 | QEITNKFLKEE | 1 | Bos taurus | K317 | LVEFTKKLPGF | 3 | Homo sapiens, Bos taurus, Mus musculus | K317 | LVEFTKRLPGF | 1 | Rattus norvegicus | K335 | QIALLKGSAVE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K353 | EIFNKKLPAGH | 2 | Mus musculus, Rattus norvegicus | K353 | EIFNKKLPSGH | 1 | Homo sapiens | K353 | EIFSKKLPAGH | 1 | Bos taurus | L301 | ENFLILTEMAT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L301 | ENFIILTEMAT | 1 | Bos taurus | L334 | DQIALLKGSAV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L354 | IFNKKLPAGHA | 2 | Mus musculus, Rattus norvegicus | L354 | IFNKKLPSGHS | 1 | Homo sapiens | L354 | IFSKKLPAGHT | 1 | Bos taurus | L361 | AGHADLLEERI | 2 | Mus musculus, Rattus norvegicus | L361 | SGHSDLLEERI | 1 | Homo sapiens | L361 | AGHTDLLEERI | 1 | Bos taurus | L362 | GHADLLEERIR | 2 | Mus musculus, Rattus norvegicus | L362 | GHSDLLEERIR | 1 | Homo sapiens | L362 | GHTDLLEERIR | 1 | Bos taurus | L465 | HHAEMLMSWRV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L465 | HHADMLMSWRV | 1 | Bos taurus | L478 | HKFTPLLCEIW | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L479 | KFTPLLCEIWD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | M279 | YNKQRMPQEIT | 2 | Homo sapiens, Mus musculus | M279 | YSKQRMPQEIT | 2 | Bos taurus, Rattus norvegicus | M304 | LILTEMATSHV | 2 | Mus musculus, Rattus norvegicus | M304 | LILTEMATNHV | 1 | Homo sapiens | M304 | IILTEMATSHV | 1 | Bos taurus | M342 | SAVEAMFLRSA | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | M379 | EYITPMFSFYK | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | M464 | HHHAEMLMSWR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M464 | HHHADMLMSWR | 1 | Bos taurus | M466 | HAEMLMSWRVN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M466 | HADMLMSWRVN | 1 | Bos taurus | N285 | PQEITNKILKE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N285 | PQEITNKFLKE | 1 | Bos taurus | N297 | FSAEENFLILT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N297 | FSAEENFIILT | 1 | Bos taurus | N307 | TEMATSHVQIL | 2 | Mus musculus, Rattus norvegicus | N307 | TEMATNHVQVL | 1 | Homo sapiens | N307 | TEMATSHVQVL | 1 | Bos taurus | P477 | DHKFTPLLCEI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Q310 | ATSHVQILVEF | 2 | Mus musculus, Rattus norvegicus | Q310 | ATNHVQVLVEF | 1 | Homo sapiens | Q310 | ATSHVQVLVEF | 1 | Bos taurus | Q323 | KLPGFQTLDHE | 3 | Homo sapiens, Bos taurus, Mus musculus | Q323 | RLPGFQTLDHE | 1 | Rattus norvegicus | Q330 | LDHEDQIALLK | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | R278 | SYNKQRMPQEI | 2 | Homo sapiens, Mus musculus | R278 | SYSKQRMPQEI | 2 | Bos taurus, Rattus norvegicus | R345 | EAMFLRSAEIF | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | R365 | DLLEERIRKSG | 3 | Bos taurus, Mus musculus, Rattus norvegicus | R365 | DLLEERIRNSG | 1 | Homo sapiens | S346 | AMFLRSAEIFN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S346 | AMFLRSAEIFS | 1 | Bos taurus | S356 | NKKLPAGHADL | 2 | Mus musculus, Rattus norvegicus | S356 | NKKLPSGHSDL | 1 | Homo sapiens | S356 | SKKLPAGHTDL | 1 | Bos taurus | S369 | ERIRKSGISDE | 3 | Bos taurus, Mus musculus, Rattus norvegicus | S369 | ERIRNSGISDE | 1 | Homo sapiens | T284 | MPQEITNKILK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T284 | MPQEITNKFLK | 1 | Bos taurus | T302 | NFLILTEMATS | 2 | Mus musculus, Rattus norvegicus | T302 | NFLILTEMATN | 1 | Homo sapiens | T302 | NFIILTEMATS | 1 | Bos taurus | V309 | MATSHVQILVE | 2 | Mus musculus, Rattus norvegicus | V309 | MATNHVQVLVE | 1 | Homo sapiens | V309 | MATSHVQVLVE | 1 | Bos taurus | V311 | TSHVQILVEFT | 2 | Mus musculus, Rattus norvegicus | V311 | TNHVQVLVEFT | 1 | Homo sapiens | V311 | TSHVQVLVEFT | 1 | Bos taurus | V313 | HVQVLVEFTKK | 2 | Homo sapiens, Bos taurus | V313 | HVQILVEFTKK | 1 | Mus musculus | V313 | HVQILVEFTKR | 1 | Rattus norvegicus | W468 | EMLMSWRVNDH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | W468 | DMLMSWRVNDH | 1 | Bos taurus | W483 | LLCEIWDVQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y375 | GISDEYITPMF | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y383 | PMFSFYKSVGE | 2 | Mus musculus, Rattus norvegicus | Y383 | PMFSFYKSIGE | 1 | Homo sapiens | Y383 | PMFSFYKSVAE | 1 | Bos taurus |
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