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mutLBSgeneDB |
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| Gene summary for SNRPD3 |
 Gene summary |
| Basic gene Info. | Gene symbol | SNRPD3 |
| Gene name | small nuclear ribonucleoprotein D3 polypeptide 18kDa | |
| Synonyms | SMD3|Sm-D3 | |
| Cytomap | UCSC genome browser: 22q11.23 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001278656.1, NM_004175.4,NR_103819.1, | |
| Description | small nuclear ribonucleoprotein Sm D3snRNP core protein D3 | |
| Modification date | 20141217 | |
| dbXrefs | MIM : 601062 | |
| HGNC : HGNC | ||
| HPRD : 03039 | ||
| Protein | UniProt: P62318 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SNRPD3 | |
| BioGPS: 6634 | ||
| Pathway | NCI Pathway Interaction Database: SNRPD3 | |
| KEGG: SNRPD3 | ||
| REACTOME: SNRPD3 | ||
| Pathway Commons: SNRPD3 | ||
| Context | iHOP: SNRPD3 | |
| ligand binding site mutation search in PubMed: SNRPD3 | ||
| UCL Cancer Institute: SNRPD3 | ||
| 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 |
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| Ligand binding site mutations for SNRPD3 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | K8 | P6S | LUSC | 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 SNRPD3 |
| 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 | K8 | P6S | -0.68342514 |
| (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 SNRPD3 from PDB |
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| Differential gene expression and gene-gene network for SNRPD3 |
| 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 SNRPD3 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0007097 | Carcinoma | 1 | Biomarker |
| umls:C0019693 | HIV Infections | 1 | Biomarker |
| umls:C0024667 | Mammary Neoplasms, Animal | 1 | Biomarker |
| umls:C0024668 | Mammary Neoplasms, Experimental | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for SNRPD3 |
| 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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| 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 SNRPD3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 2y9d | R | K8 |
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| Conservation information for LBS of SNRPD3 |
| Multiple alignments for P62318 in multiple species |
| LBS | AA sequence | # species | Species | D52 | TVTYRDGRVAQ | 2 | Homo sapiens, Mus musculus | D52 | TYTAKDGKVSQ | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D52 | VVTFRDGRSHQ | 1 | Caenorhabditis elegans | D52 | SVTARDGRVSH | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | D52 | TVTYRDGRTAN | 1 | Drosophila melanogaster | G65 | QVYIRGSKIRF | 2 | Homo sapiens, Mus musculus | G65 | HVFIRGSLVRF | 1 | Arabidopsis thaliana | G65 | HVFIRGSKVRF | 1 | Arabidopsis thaliana | G65 | NVFIRGNKIRF | 1 | Caenorhabditis elegans | G65 | QVYIRGSHIRF | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | G65 | NVYIRGSKIRF | 1 | Drosophila melanogaster | K8 | IGVPIKVLHEA | 3 | Homo sapiens, Mus musculus, Drosophila melanogaster | K8 | LGIPVKLLHES | 1 | Arabidopsis thaliana | K8 | LGIPVKLLHEA | 1 | Arabidopsis thaliana | K8 | VGVPIKILHEA | 1 | Caenorhabditis elegans | K8 | MSLCIKLLHET | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | M39 | EAEDNMNCQMS | 2 | Homo sapiens, Mus musculus | M39 | ECEDNWNCQLE | 2 | Arabidopsis thaliana, Arabidopsis thaliana | M39 | EAEDNMNCQLA | 1 | Caenorhabditis elegans | M39 | EAEDNMNCQMR | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | M39 | EAEDNMNCQMT | 1 | Drosophila melanogaster | M82 | LKNAPMLK--- | 2 | Homo sapiens, Mus musculus | M82 | LKNAPMFK--- | 2 | Caenorhabditis elegans, Drosophila melanogaster | M82 | LKNAPMFK--D | 1 | Arabidopsis thaliana | M82 | LKHAPMFKRLD | 1 | Arabidopsis thaliana | M82 | LRNAPMFK--- | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | N38 | IEAEDNMNCQM | 4 | Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Mus musculus, Drosophila melanogaster | N38 | IECEDNWNCQL | 2 | Arabidopsis thaliana, Arabidopsis thaliana | N38 | SEAEDNMNCQL | 1 | Caenorhabditis elegans | N40 | AEDNMNCQMSN | 2 | Homo sapiens, Mus musculus | N40 | CEDNWNCQLEN | 1 | Arabidopsis thaliana | N40 | CEDNWNCQLED | 1 | Arabidopsis thaliana | N40 | AEDNMNCQLAE | 1 | Caenorhabditis elegans | N40 | AEDNMNCQMRD | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | N40 | AEDNMNCQMTQ | 1 | Drosophila melanogaster | R51 | ITVTYRDGRVA | 2 | Homo sapiens, Mus musculus | R51 | ITYTAKDGKVS | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R51 | TVVTFRDGRSH | 1 | Caenorhabditis elegans | R51 | ISVTARDGRVS | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | R51 | ITVTYRDGRTA | 1 | Drosophila melanogaster | R64 | EQVYIRGSKIR | 2 | Homo sapiens, Mus musculus | R64 | EHVFIRGSLVR | 1 | Arabidopsis thaliana | R64 | EHVFIRGSKVR | 1 | Arabidopsis thaliana | R64 | DNVFIRGNKIR | 1 | Caenorhabditis elegans | R64 | DQVYIRGSHIR | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | R64 | ENVYIRGSKIR | 1 | Drosophila melanogaster | S66 | VYIRGSKIRFL | 3 | Homo sapiens, Mus musculus, Drosophila melanogaster | S66 | VFIRGSLVRFL | 1 | Arabidopsis thaliana | S66 | VFIRGSKVRFM | 1 | Arabidopsis thaliana | S66 | VFIRGNKIRFM | 1 | Caenorhabditis elegans | S66 | VYIRGSHIRFL | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) |
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