Task 7: Research SNPs
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Contents
HGMD (The Human Gene Mutation Database)
The results for the HFE gene contain the following types of mutations:
| mutation type | definition | number |
|---|---|---|
| missense, nonsense | mutation that leads to a change of amino acid or a stop codon | 28 |
| splicing | mutation that affects mRNA splicing | 3 |
| regulatory | substitiution causing abnormal regulation | 1 |
| small deletion | micro deletion (<= 20 bp) | 4 |
| small insertion | micro insertions (<= 20 bp) | 1 |
| small indel | micro indels (<= 20 bp) | 0 |
| gross deletion | delition > 20 bp | 2 |
| gross insertions/duplications | insertion > 20bp | 0 |
| complex rearrangments | rearrangements of stretches of the DNA sequence | 1 |
| repeat variations | differences in repeat length | 0 |
- total in public 40
- non public 49
missense, nonsens mutations for HFE
| accession number | codon change | aa change | codon number |
|---|---|---|---|
| CM032270 | AGGc-AGC | Arg-Ser | 6 |
| CM091838 | TTG-TGG | Leu-Trp | 46 |
| CM994469 | cGTG-ATG | Val-Met | 53 |
| CM994470 | cGTG-ATG | Val-Met | 59 |
| HM971246 | CATg-CAC | His-His | 63 |
| CM960827 | tCAT-GAT | His-Asp | 63 |
| CM990718 | gAGT-TGT | Ser-Cys | 65 |
| CM033969 | tCGC-TGC | Arg-Cys | 66 |
| CM020721 | cCGA-TGA | Arg-Term | 71 |
| CM990719 | aGGG-CGG | Gly-Arg | 93 |
| CM990720 | ATT-ACT | Ile-Thr | 105 |
| CM990721 | CAAg-CAC | Gln-His | 127 |
| CM091839 | aGAC-AAC | Asp-Asn | 129 |
| CM091840 | TACg-TAG | Tyr-Term | 138 |
| CM004810 | gGAG-CAG | Glu-Gln | 168 |
| CM004106 | gGAG-TAG | Glu-Term | 168 |
| CM004107 | TGG-TAG | Trp-Term | 169 |
| CM015326 | GCC-GTC | Ala-Val | 176 |
| CM081301 | CTG-CCG | Leu-Pro | 183 |
| CM034097 | CGG-CAG | Arg-Gln | 224 |
| CM101181 | cCAG-TAG | Gln-Term | 233 |
| CM024530 | tGTA-TTA | Val-Leu | 272 |
| CM994771 | aGAG-AAG | Glu-Lys | 277 |
| CM960828 | TGC-TAC | Cys-Tyr | 282 |
| CM004391 | TGC-TCC | Cys-Ser | 282 |
| CM032271 | CAG-CCG | Gln-Pro | 283 |
| HM030028 | GTG-GCG | Val-Ala | 295 |
| CM990722 | AGG-ATG | Arg-Met | 330 |
dbSNP
Results
synonymous SNPS in coding region of isoform 1 human and transcript variant 1
| cluster ID | MAF | SNP allel | residue | codon position | aa position |
|---|---|---|---|---|---|
| rs114758821 | 9E-4 | G -> A | Pro | 3 | 7 |
| rs147297176 | 5E-4 | C -> T | Phe | 3 | 58 |
| rs147426902 | 3.2E-3 | T -> C | His | 3 | 63 |
| rs62625342 | 5E-4 | C -> T | Ser | 3 | 76 |
| rs148480830 | - | C -> G | Ala | 3 | 162 |
| rs182920795 | 5E-4 | T -> A | Pro | 3 | 253 |
| rs201310322 | - | C -> T | Pro | 3 | 292 |
| rs114038675 | 5E-4 | G -> A | Glu | 3 | 298 |
| rs148632352 | - | T -> C | Val | 3 | 315 |
| rs35201683 | 6.4E-3 | C -> T | Tyr | 3 | 342 |
SNPdbe
Comparison of databases
| database | last update | version | what information | where from | # entries homo sapiens | # s SNPs | # ns SNPs | # disease causing SNPs | # SNPs in UTR | total |
|---|---|---|---|---|---|---|---|---|---|---|
| HGMD | spring 2013 | public 2013.1 (mainly 3 year old data) | Collection of published gene lesions in the human genome that cause inherited diseases. | Only from publications. Journals are searched manually and by computational means each week. | 99869 | |||||
| dbSNP | 26.06.2012 | Build 137 | short nucleotide sequence variations in different organisms | 192,678,553 | 10 | 41 | 10 | 162 | 213 | |
| SNPdbe | 05.03.2012 | - | 967879 |
Mutation map
References
Stenson et al (2009), The Human Gene Mutation Database (HGMD®): 2008 Update. Genome Med 1(1):13
ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_SNP.pdf
