|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for SNRPD1 |
 Gene summary |
| Basic gene Info. | Gene symbol | SNRPD1 |
| Gene name | small nuclear ribonucleoprotein D1 polypeptide 16kDa | |
| Synonyms | HsT2456|SMD1|SNRPD|Sm-D1 | |
| Cytomap | UCSC genome browser: 18q11.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001291916.1, NM_006938.3, | |
| Description | Sm-D autoantigensmall nuclear ribonucleoprotein D1 polypeptide 16kDa pseudogenesmall nuclear ribonucleoprotein Sm D1snRNP core protein D1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601063 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000167088 | ||
| HPRD : 03040 | ||
| Vega : OTTHUMG00000178934 | ||
| Protein | UniProt: P62314 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SNRPD1 | |
| BioGPS: 6632 | ||
| Pathway | NCI Pathway Interaction Database: SNRPD1 | |
| KEGG: SNRPD1 | ||
| REACTOME: SNRPD1 | ||
| Pathway Commons: SNRPD1 | ||
| Context | iHOP: SNRPD1 | |
| ligand binding site mutation search in PubMed: SNRPD1 | ||
| UCL Cancer Institute: SNRPD1 | ||
| 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 | GO:0000387 | spliceosomal snRNP assembly | 18984161 |
| Top |
| Ligand binding site mutations for SNRPD1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | S35 | L35V | LUSC | 1 | R66 | R67C | STAD | 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. |
| Top |
| Protein structure related information for SNRPD1 |
| 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 |
 |
| 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 SNRPD1 from PDB |
| Top |
| Differential gene expression and gene-gene network for SNRPD1 |
| 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) |
| Top |
| Top |
| Phenotype information for SNRPD1 |
| 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 |
| Top |
| Pharmacological information for SNRPD1 |
| 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. |
 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of SNRPD1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 4pjo | C | S35 R66 | NUC | Nucleic Acids | 4pjo | c | S35 R66 | NUC | Nucleic Acids | 4pjo | Q | S35 R66 | NUC | Nucleic Acids | 4pjo | q | S35 R66 |
| Top |
| Conservation information for LBS of SNRPD1 |
| Multiple alignments for P62314 in multiple species |
| LBS | AA sequence | # species | Species | E18 | ETVTIELKNGT | 4 | Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster | E18 | ETVNIELKNGT | 1 | Caenorhabditis elegans | E18 | ETVSIELKNGT | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | G22 | IELKNGTQVHG | 3 | Homo sapiens, Bos taurus, Mus musculus | G22 | IELKNGTQVSG | 1 | Caenorhabditis elegans | G22 | IELKNGTIVHG | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | G22 | IELKNGTQIHG | 1 | Drosophila melanogaster | G62 | TLSIRGNNIRY | 6 | Homo sapiens, Caenorhabditis elegans, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Mus musculus, Drosophila melanogaster | K2 | 6 | Homo sapiens, Caenorhabditis elegans, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Mus musculus, Drosophila melanogaster | K20 | VTIELKNGTQV | 3 | Homo sapiens, Bos taurus, Mus musculus | K20 | VNIELKNGTQV | 1 | Caenorhabditis elegans | K20 | VSIELKNGTIV | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | K20 | VTIELKNGTQI | 1 | Drosophila melanogaster | K48 | VKMTLKNREPV | 3 | Homo sapiens, Bos taurus, Mus musculus | K48 | VSMTVKNKEPV | 1 | Caenorhabditis elegans | K48 | VKMTVKGREPV | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | K48 | VRMTIKNRDPV | 1 | Drosophila melanogaster | L19 | TVTIELKNGTQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster | L19 | TVNIELKNGTQ | 1 | Caenorhabditis elegans | L19 | TVSIELKNGTI | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | M1 | 6 | Homo sapiens, Caenorhabditis elegans, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Mus musculus, Drosophila melanogaster | M36 | GVDVSMNTHLK | 3 | Homo sapiens, Bos taurus, Mus musculus | M36 | GVDVAMNTHLR | 1 | Caenorhabditis elegans | M36 | SVDMQMNTHLK | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | M36 | GVDVAMNTHLK | 1 | Drosophila melanogaster | N21 | TIELKNGTQVH | 3 | Homo sapiens, Bos taurus, Mus musculus | N21 | NIELKNGTQVS | 1 | Caenorhabditis elegans | N21 | SIELKNGTIVH | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | N21 | TIELKNGTQIH | 1 | Drosophila melanogaster | N37 | VDVSMNTHLKA | 3 | Homo sapiens, Bos taurus, Mus musculus | N37 | VDVAMNTHLRA | 1 | Caenorhabditis elegans | N37 | VDMQMNTHLKA | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | N37 | VDVAMNTHLKS | 1 | Drosophila melanogaster | N49 | KMTLKNREPVQ | 3 | Homo sapiens, Bos taurus, Mus musculus | N49 | SMTVKNKEPVK | 1 | Caenorhabditis elegans | N49 | KMTVKGREPVP | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | N49 | RMTIKNRDPVH | 1 | Drosophila melanogaster | N63 | LSIRGNNIRYF | 4 | Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster | N63 | LSIRGNNIRYI | 1 | Caenorhabditis elegans | N63 | LSIRGNNIRYY | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | R50 | MTLKNREPVQL | 3 | Homo sapiens, Bos taurus, Mus musculus | R50 | MTVKNKEPVKL | 1 | Caenorhabditis elegans | R50 | MTVKGREPVPV | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | R50 | MTIKNRDPVHL | 1 | Drosophila melanogaster | R61 | ETLSIRGNNIR | 5 | Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Mus musculus, Drosophila melanogaster | R61 | DTLSIRGNNIR | 1 | Caenorhabditis elegans | R66 | RGNNIRYFILP | 4 | Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster | R66 | RGNNIRYIILP | 1 | Caenorhabditis elegans | R66 | RGNNIRYYILP | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | S35 | TGVDVSMNTHL | 3 | Homo sapiens, Bos taurus, Mus musculus | S35 | MGVDVAMNTHL | 1 | Caenorhabditis elegans | S35 | TSVDMQMNTHL | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | S35 | TGVDVAMNTHL | 1 | Drosophila melanogaster | V34 | ITGVDVSMNTH | 3 | Homo sapiens, Bos taurus, Mus musculus | V34 | IMGVDVAMNTH | 1 | Caenorhabditis elegans | V34 | ITSVDMQMNTH | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | V34 | ITGVDVAMNTH | 1 | Drosophila melanogaster | V4 | 6 | Homo sapiens, Caenorhabditis elegans, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Mus musculus, Drosophila melanogaster |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |