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mutLBSgeneDB |
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| Gene summary for APLF |
 Gene summary |
| Basic gene Info. | Gene symbol | APLF |
| Gene name | aprataxin and PNKP like factor | |
| Synonyms | APFL|C2orf13|PALF|Xip1|ZCCHH1 | |
| Cytomap | UCSC genome browser: 2p13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_173545.2, | |
| Description | PNK and APTX-like FHA domain-containing proteinPNK and APTX-like FHA proteinXRCC1-interacting protein 1aprataxin and PNK-like factoraprataxin- and PNK-like factorapurinic-apyrimidinic endonuclease APLFzinc finger, CX5CX6HX5H motif containing 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 611035 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000169621 | ||
| HPRD : 09848 | ||
| Vega : OTTHUMG00000129566 | ||
| Protein | UniProt: Q8IW19 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APLF | |
| BioGPS: 200558 | ||
| Pathway | NCI Pathway Interaction Database: APLF | |
| KEGG: APLF | ||
| REACTOME: APLF | ||
| Pathway Commons: APLF | ||
| Context | iHOP: APLF | |
| ligand binding site mutation search in PubMed: APLF | ||
| UCL Cancer Institute: APLF | ||
| 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:0000737 | DNA catabolic process, endonucleolytic | 17396150 | GO:0006974 | cellular response to DNA damage stimulus | 17396150 | GO:0090305 | nucleic acid phosphodiester bond hydrolysis | 17396150 |
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| Ligand binding site mutations for APLF |
| 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 | R37 | R37S | BRCA | 1 | T59 | T59R | GBM | 1 | Y423 | P422A | HNSC | 1 | N431 | Q433L | LUSC | 1 | H398 | P399S | SKCM | 1 | H392 | P390S | SKCM | 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 APLF |
| 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 | Y423 | P422A | -1.5488551 | R37 | R37S | -1.4850773 | H392 | P390S | -1.0870076 | N431 | Q433L | -0.86357565 | H398 | P399S | -0.77292815 | T59 | T59R | -0.45405416 |
| (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 APLF from PDB |
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| Differential gene expression and gene-gene network for APLF |
| 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 APLF |
| 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 APLF |
| 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 APLF go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2kqb | A | H392 H398 | ZN | ZINC(2+) | 2kqd | A | H392 H398 | ZN | ZINC(2+) | 2kuo | A | H392 H398 | III | Peptide ligand (TYR,ASP,GLU,SEP,TPO,ASP,GLU) | 5e50 | A | R37 T59 | ADN | ADENOSINE | 2kqe | A | Y423 | RIB | RIBOSE | 2kqe | A | Y423 N431 |
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| Conservation information for LBS of APLF |
| Multiple alignments for Q8IW19 in multiple species |
| LBS | AA sequence | # species | Species | C379 | VKRTSCMYGAN | 1 | Homo sapiens | C379 | VRRTACMYGAN | 1 | Mus musculus | C379 | VQRTSCMYGAN | 1 | Bos taurus | C385 | MYGANCYRKNP | 2 | Homo sapiens, Bos taurus | C385 | MYGANCYRRNP | 1 | Mus musculus | G28 | TVIGRGPLLGI | 2 | Homo sapiens, Mus musculus | G28 | TVIGRGPLLG- | 1 | Bos taurus | G382 | TSCMYGANCYR | 2 | Homo sapiens, Bos taurus | G382 | TACMYGANCYR | 1 | Mus musculus | H392 | RKNPVHFQHFS | 2 | Homo sapiens, Bos taurus | H392 | RRNPLHFQHFS | 1 | Mus musculus | H398 | FQHFSHPGDSD | 3 | Homo sapiens, Mus musculus, Bos taurus | H58 | RIKPIHTNPCF | 1 | Homo sapiens | H58 | RIKPIHRNPCF | 1 | Mus musculus | H58 | ----LHRNPCY | 1 | Bos taurus | I33 | GPLLGITDKRV | 2 | Homo sapiens, Mus musculus | I33 | GPLLG------ | 1 | Bos taurus | K36 | LGITDKRVSRR | 2 | Homo sapiens, Mus musculus | K36 | LG--------- | 1 | Bos taurus | M380 | KRTSCMYGANC | 1 | Homo sapiens | M380 | RRTACMYGANC | 1 | Mus musculus | M380 | QRTSCMYGANC | 1 | Bos taurus | N384 | CMYGANCYRKN | 2 | Homo sapiens, Bos taurus | N384 | CMYGANCYRRN | 1 | Mus musculus | N431 | SCYRKNPQHKI | 2 | Homo sapiens, Bos taurus | N431 | SCYRKNPQHKM | 1 | Mus musculus | N60 | KPIHTNPCFYQ | 1 | Homo sapiens | N60 | KPIHRNPCFYQ | 1 | Mus musculus | N60 | --LHRNPCYYQ | 1 | Bos taurus | P29 | VIGRGPLLGIT | 2 | Homo sapiens, Mus musculus | P29 | VIGRGPLLG-- | 1 | Bos taurus | R27 | ETVIGRGPLLG | 2 | Homo sapiens, Bos taurus | R27 | QTVIGRGPLLG | 1 | Mus musculus | R37 | GITDKRVSRRH | 2 | Homo sapiens, Mus musculus | R37 | G---------- | 1 | Bos taurus | R387 | GANCYRKNPVH | 2 | Homo sapiens, Bos taurus | R387 | GANCYRRNPLH | 1 | Mus musculus | R40 | DKRVSRRHAIL | 2 | Homo sapiens, Mus musculus | R40 | ----------- | 1 | Bos taurus | R429 | GASCYRKNPQH | 2 | Mus musculus, Bos taurus | R429 | GPSCYRKNPQH | 1 | Homo sapiens | S39 | TDKRVSRRHAI | 2 | Homo sapiens, Mus musculus | S39 | ----------- | 1 | Bos taurus | S426 | CPYGASCYRKN | 2 | Mus musculus, Bos taurus | S426 | CPYGPSCYRKN | 1 | Homo sapiens | T34 | PLLGITDKRVS | 2 | Homo sapiens, Mus musculus | T34 | PLLG------- | 1 | Bos taurus | T59 | IKPIHTNPCFY | 1 | Homo sapiens | T59 | IKPIHRNPCFY | 1 | Mus musculus | T59 | ---LHRNPCYY | 1 | Bos taurus | Y381 | RTSCMYGANCY | 2 | Homo sapiens, Bos taurus | Y381 | RTACMYGANCY | 1 | Mus musculus | Y386 | YGANCYRKNPV | 2 | Homo sapiens, Bos taurus | Y386 | YGANCYRRNPL | 1 | Mus musculus | Y423 | RPECPYGASCY | 2 | Mus musculus, Bos taurus | Y423 | RPECPYGPSCY | 1 | Homo sapiens |
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