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mutLBSgeneDB |
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| Gene summary for PHYHD1 |
 Gene summary |
| Basic gene Info. | Gene symbol | PHYHD1 |
| Gene name | phytanoyl-CoA dioxygenase domain containing 1 | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 9q34.11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001100876.1, NM_001100877.1,NM_174933.3, | |
| Description | phytanoyl-CoA dioxygenase domain-containing protein 1 | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000175287 | ||
| HPRD : 17850 | ||
| Vega : OTTHUMG00000020764 | ||
| Protein | UniProt: Q5SRE7 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PHYHD1 | |
| BioGPS: 254295 | ||
| Pathway | NCI Pathway Interaction Database: PHYHD1 | |
| KEGG: PHYHD1 | ||
| REACTOME: PHYHD1 | ||
| Pathway Commons: PHYHD1 | ||
| Context | iHOP: PHYHD1 | |
| ligand binding site mutation search in PubMed: PHYHD1 | ||
| UCL Cancer Institute: PHYHD1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for PHYHD1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D158 | A159T | COAD | 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 PHYHD1 |
| 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 | D158 | A159T | -0.79620964 |
| (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 PHYHD1 from PDB |
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| Differential gene expression and gene-gene network for PHYHD1 |
| 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 PHYHD1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PHYHD1 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PHYHD1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | AKG | 2-OXOGLUTARIC ACID | 3obz | A | D158 | FE2 | IRON(2+) | 3obz | A | D158 |
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| Conservation information for LBS of PHYHD1 |
| Multiple alignments for Q5SRE7 in multiple species |
| LBS | AA sequence | # species | Species | D158 | VSPHQDATFLY | 2 | Mus musculus, Rattus norvegicus | D158 | VSPHQDASFLY | 1 | Homo sapiens | D158 | VVPHQDNSFVY | 1 | Arabidopsis thaliana | D158 | VVPHQDNTFLY | 1 | Oryza sativa subsp. japonica | D158 | VTDHVDSTFLR | 1 | Caenorhabditis elegans | D158 | VTPHQDATFLY | 1 | Danio rerio | D158 | VAPHQDASFLY | 1 | Bos taurus | H156 | GEVSPHQDATF | 2 | Mus musculus, Rattus norvegicus | H156 | GEVSPHQDASF | 1 | Homo sapiens | H156 | GEVVPHQDNSF | 1 | Arabidopsis thaliana | H156 | GEVVPHQDNTF | 1 | Oryza sativa subsp. japonica | H156 | GAVTDHVDSTF | 1 | Caenorhabditis elegans | H156 | GEVTPHQDATF | 1 | Danio rerio | H156 | GEVAPHQDASF | 1 | Bos taurus | H246 | HGEVVHKSEQN | 3 | Mus musculus, Rattus norvegicus, Bos taurus | H246 | HGEVVHKSKQN | 1 | Homo sapiens | H246 | HGDLIHQSFEN | 1 | Arabidopsis thaliana | H246 | HGDLVHQSFEN | 1 | Oryza sativa subsp. japonica | H246 | HGLVVHKSEAN | 1 | Caenorhabditis elegans | H246 | HGEVVHRSAAN | 1 | Danio rerio | I143 | VQSMYIFKQPH | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | I143 | MQSMYIFKQPG | 1 | Arabidopsis thaliana | I143 | IQSMYIFKQPG | 1 | Oryza sativa subsp. japonica | I143 | VQSMYIFKQPK | 1 | Caenorhabditis elegans | I143 | LQSMYIFKQPG | 1 | Danio rerio | K145 | SMYIFKQPHFG | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | K145 | SMYIFKQPGIG | 3 | Arabidopsis thaliana, Oryza sativa subsp. japonica, Danio rerio | K145 | SMYIFKQPKIG | 1 | Caenorhabditis elegans | L187 | LENGCLWFIPG | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | L187 | LVNGCLWAIPG | 1 | Arabidopsis thaliana | L187 | KTNGCLWAIPG | 1 | Oryza sativa subsp. japonica | L187 | VENGCLSFIPG | 1 | Caenorhabditis elegans | L187 | QENGCLWFIPG | 1 | Danio rerio | R257 | LSDRSRQAYTF | 2 | Homo sapiens, Bos taurus | R257 | LSSKSRHAYSL | 1 | Arabidopsis thaliana | R257 | LSLVSRHALSL | 1 | Oryza sativa subsp. japonica | R257 | TSEKSRHAYTI | 1 | Caenorhabditis elegans | R257 | TSDASRHVYTF | 1 | Danio rerio | R257 | HSDHSRQAYTV | 1 | Mus musculus | R257 | LSDHSRQAYTF | 1 | Rattus norvegicus | S248 | EVVHKSEQNLS | 2 | Rattus norvegicus, Bos taurus | S248 | EVVHKSKQNLS | 1 | Homo sapiens | S248 | DLIHQSFENLS | 1 | Arabidopsis thaliana | S248 | DLVHQSFENLS | 1 | Oryza sativa subsp. japonica | S248 | LVVHKSEANTS | 1 | Caenorhabditis elegans | S248 | EVVHRSAANTS | 1 | Danio rerio | S248 | EVVHKSEQNHS | 1 | Mus musculus | T261 | SRQAYTFHLME | 3 | Homo sapiens, Rattus norvegicus, Bos taurus | T261 | SRHAYSLHVVE | 1 | Arabidopsis thaliana | T261 | SRHALSLHVID | 1 | Oryza sativa subsp. japonica | T261 | SRHAYTIHVME | 1 | Caenorhabditis elegans | T261 | SRHVYTFHIME | 1 | Danio rerio | T261 | SRQAYTVHLME | 1 | Mus musculus | W174 | RVLGVWIAVED | 1 | Homo sapiens | W174 | SCTGLWIALED | 1 | Arabidopsis thaliana | W174 | SCTGLWLALED | 1 | Oryza sativa subsp. japonica | W174 | HLTGVWIAIDE | 1 | Caenorhabditis elegans | W174 | RVMGVWVALED | 1 | Danio rerio | W174 | RVLGLWIAMED | 1 | Mus musculus | W174 | RVLGLWIATED | 1 | Rattus norvegicus | W174 | RVLGLWIALED | 1 | Bos taurus |
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