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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for FAM20A |
 Gene summary |
| Gene information | Gene symbol | FAM20A | Gene ID | 54757 |
| Gene name | FAM20A, golgi associated secretory pathway pseudokinase | |
| Synonyms | AI1G|AIGFS|FP2747 | |
| Cytomap | 17q24.2 | |
| Type of gene | protein-coding | |
| Description | pseudokinase FAM20Afamily with sequence similarity 20, member Aprotein FAM20A | |
| Modification date | 20180523 | |
| UniProtAcc | Q96MK3 | |
| Context | PubMed: FAM20A [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| FAM20A | GO:0001934 | positive regulation of protein phosphorylation | 25789606 |
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Exon skipping events across known transcript of Ensembl for FAM20A from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for FAM20A |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for FAM20A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_292771 | 17 | 66535477:66535537:66536025:66536107:66539769:66539810 | 66536025:66536107 | ENSG00000108950.7 | ENST00000590873.1 |
| exon_skip_292775 | 17 | 66536025:66536107:66536687:66536864:66536989:66537067 | 66536687:66536864 | ENSG00000108950.7 | ENST00000375556.4 |
| exon_skip_292785 | 17 | 66536025:66536107:66536989:66537099:66538125:66538306 | 66536989:66537099 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1 |
| exon_skip_292788 | 17 | 66536025:66536107:66536989:66537124:66538125:66538306 | 66536989:66537124 | ENSG00000108950.7 | ENST00000226094.5 |
| exon_skip_292805 | 17 | 66537051:66537124:66538125:66538306:66538834:66538950 | 66538125:66538306 | ENSG00000108950.7 | ENST00000226094.5,ENST00000592847.1 |
| exon_skip_292808 | 17 | 66538125:66538306:66538834:66538950:66539769:66539810 | 66538834:66538950 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1,ENST00000226094.5,ENST00000592847.1 |
| exon_skip_292809 | 17 | 66539769:66539858:66548013:66548092:66550917:66550968 | 66548013:66548092 | ENSG00000108950.7 | ENST00000226094.5 |
| exon_skip_292810 | 17 | 66539769:66539862:66548013:66548092:66550917:66550968 | 66548013:66548092 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1,ENST00000592847.1 |
| exon_skip_292813 | 17 | 66548013:66548092:66550917:66550968:66551699:66551884 | 66550917:66550968 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1,ENST00000226094.5,ENST00000592847.1 |
| exon_skip_292814 | 17 | 66551699:66551884:66586264:66586490:66596403:66596737 | 66586264:66586490 | ENSG00000108950.7 | ENST00000590074.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for FAM20A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_292771 | 17 | 66535477:66535537:66536025:66536107:66539769:66539810 | 66536025:66536107 | ENSG00000108950.7 | ENST00000590873.1 |
| exon_skip_292775 | 17 | 66536025:66536107:66536687:66536864:66536989:66537067 | 66536687:66536864 | ENSG00000108950.7 | ENST00000375556.4 |
| exon_skip_292785 | 17 | 66536025:66536107:66536989:66537099:66538125:66538306 | 66536989:66537099 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1 |
| exon_skip_292788 | 17 | 66536025:66536107:66536989:66537124:66538125:66538306 | 66536989:66537124 | ENSG00000108950.7 | ENST00000226094.5 |
| exon_skip_292805 | 17 | 66537051:66537124:66538125:66538306:66538834:66538950 | 66538125:66538306 | ENSG00000108950.7 | ENST00000226094.5,ENST00000592847.1 |
| exon_skip_292808 | 17 | 66538125:66538306:66538834:66538950:66539769:66539810 | 66538834:66538950 | ENSG00000108950.7 | ENST00000226094.5,ENST00000592554.1,ENST00000590074.1,ENST00000592847.1 |
| exon_skip_292809 | 17 | 66539769:66539858:66548013:66548092:66550917:66550968 | 66548013:66548092 | ENSG00000108950.7 | ENST00000226094.5 |
| exon_skip_292810 | 17 | 66539769:66539862:66548013:66548092:66550917:66550968 | 66548013:66548092 | ENSG00000108950.7 | ENST00000592554.1,ENST00000590074.1,ENST00000592847.1 |
| exon_skip_292813 | 17 | 66548013:66548092:66550917:66550968:66551699:66551884 | 66550917:66550968 | ENSG00000108950.7 | ENST00000226094.5,ENST00000592554.1,ENST00000590074.1,ENST00000592847.1 |
| exon_skip_292814 | 17 | 66551699:66551884:66586264:66586490:66596403:66596737 | 66586264:66586490 | ENSG00000108950.7 | ENST00000590074.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for FAM20A |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000592554 | 66536989 | 66537099 | Frame-shift |
| ENST00000592554 | 66538834 | 66538950 | Frame-shift |
| ENST00000592554 | 66548013 | 66548092 | Frame-shift |
| ENST00000592554 | 66550917 | 66550968 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000592554 | 66536989 | 66537099 | Frame-shift |
| ENST00000592554 | 66538834 | 66538950 | Frame-shift |
| ENST00000592554 | 66548013 | 66548092 | Frame-shift |
| ENST00000592554 | 66550917 | 66550968 | In-frame |
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Infer the effects of exon skipping event on protein functional features for FAM20A |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000592554 | 2972 | 541 | 66550917 | 66550968 | 1313 | 1363 | 196 | 213 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000592554 | 2972 | 541 | 66550917 | 66550968 | 1313 | 1363 | 196 | 213 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q96MK3 | 196 | 213 | 193 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 206 | 208 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 34 | 541 | Chain | ID=PRO_0000008743;Note=Pseudokinase FAM20A |
| Q96MK3 | 196 | 213 | 200 | 203 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 197 | 214 | Natural variant | ID=VAR_066859;Note=In AI1G. DYSQDEKALLGACDCTQI->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21990045;Dbxref=PMID:21990045 |
| Q96MK3 | 196 | 213 | 212 | 214 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q96MK3 | 196 | 213 | 193 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 206 | 208 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 34 | 541 | Chain | ID=PRO_0000008743;Note=Pseudokinase FAM20A |
| Q96MK3 | 196 | 213 | 200 | 203 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
| Q96MK3 | 196 | 213 | 197 | 214 | Natural variant | ID=VAR_066859;Note=In AI1G. DYSQDEKALLGACDCTQI->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21990045;Dbxref=PMID:21990045 |
| Q96MK3 | 196 | 213 | 212 | 214 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5WRR |
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SNVs in the skipped exons for FAM20A |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_292771 | 66536026 | 66536107 | 66536063 | 66536063 | Frame_Shift_Del | C | - | p.D423fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_292805 | 66538126 | 66538306 | 66538161 | 66538161 | Frame_Shift_Del | G | - | p.P358fs |
| KIRP | TCGA-GL-6846-01 | exon_skip_292808 | 66538835 | 66538950 | 66538845 | 66538846 | Frame_Shift_Del | AA | - | p.306_307del |
| KIRP | TCGA-GL-6846-01 | exon_skip_292808 | 66538835 | 66538950 | 66538845 | 66538846 | Frame_Shift_Del | AA | - | p.F306fs |
| LIHC | TCGA-RC-A7SH-01 | exon_skip_292808 | 66538835 | 66538950 | 66538937 | 66538937 | Frame_Shift_Del | G | - | p.R276fs |
| UCS | TCGA-NA-A4QW-01 | exon_skip_292808 | 66538835 | 66538950 | 66538939 | 66538955 | Frame_Shift_Del | AAGTCCAGAATCCTGCA | - | p.271_275del |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_292813 | 66550918 | 66550968 | 66550936 | 66550936 | Frame_Shift_Del | C | - | p.A208fs |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| MCC142_SKIN | 66548014 | 66548092 | 66548079 | 66548079 | Frame_Shift_Del | A | - | p.S218fs |
| C33A_CERVIX | 66536026 | 66536107 | 66536075 | 66536075 | Missense_Mutation | T | C | p.T418A |
| MDAMB453_BREAST | 66536026 | 66536107 | 66536084 | 66536084 | Missense_Mutation | C | T | p.E415K |
| HEC1A_ENDOMETRIUM | 66536990 | 66537124 | 66537037 | 66537037 | Missense_Mutation | T | C | p.Q391R |
| HEC1A_ENDOMETRIUM | 66536990 | 66537099 | 66537037 | 66537037 | Missense_Mutation | T | C | p.Q391R |
| KYSE450_OESOPHAGUS | 66536990 | 66537124 | 66537040 | 66537040 | Missense_Mutation | C | T | p.S390N |
| KYSE450_OESOPHAGUS | 66536990 | 66537099 | 66537040 | 66537040 | Missense_Mutation | C | T | p.S390N |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66536990 | 66537124 | 66537092 | 66537092 | Missense_Mutation | C | G | p.V373L |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66536990 | 66537099 | 66537092 | 66537092 | Missense_Mutation | C | G | p.V373L |
| DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 66538126 | 66538306 | 66538154 | 66538154 | Missense_Mutation | G | A | p.R361C |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66538126 | 66538306 | 66538303 | 66538303 | Missense_Mutation | C | T | p.S311N |
| JHUEM7_ENDOMETRIUM | 66538835 | 66538950 | 66538847 | 66538847 | Missense_Mutation | A | C | p.F306V |
| NCIH292_LUNG | 66538126 | 66538306 | 66538126 | 66538126 | Splice_Site | T | G | p.E370A |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 66538126 | 66538306 | 66538305 | 66538305 | Splice_Site | C | A | p.A310A |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FAM20A |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FAM20A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FAM20A |
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RelatedDrugs for FAM20A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for FAM20A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| FAM20A | C2931783 | Amelogenesis imperfecta nephrocalcinosis | 3 | ORPHANET;UNIPROT |
| FAM20A | C3495559 | Juvenile arthritis | 1 | CTD_human |
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