Researching SNPs (Phenylketonuria)

Summary

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Research SNPs

HGMD

HGMD (The Human Gene Mutation Database) is a disease associated mutation database available for scientists. ... <ref name="hgmd"> Peter D. Stenson, Matthew Mort, Edward V. Ball, Katy Howells, Andrew D. Phillips, Nick S. T. Thomas and David N. Cooper (2009): "[ The Human Gene Mutation Database: 2008 update]". Genome Medicine 1: 13. doi:10.1186/gm13 </ref>

<figtable id="hgmd">

Mutation types for PAH found in HGMD with appendant quantity and definition
Mutation type	# of mutations	Definition
Missense/nonsense	415	x
Splicing	82	x
Regulatory	1	x
Small deletions	66	x
Small insertions	8	x
Small indels	6	x
Gross deletions	27	x
Gross insertions/duplications	3	x
Complex rearrangements	1	x
Repeat variations	0	no mutations
Total Number of mutations: 609 (HGMD professional 2013.1: 720)

</figtable> 543 mutations of the table above are known for causing Phenylketonuria, 58 for Hyperphenylalaninaemia, one for Increased activity and one for association with Schizophrenia. For five of the mutations it is assumed that they cause Phenylketonuria and one Hyperphenylalaninanaemia.

TODO:Three-letter to one-letter amino acid code (NCBI sequence is not the same as HGMD sequence!!!!) --> own script?

dbSNP

dbSNP (Short Genetic Variations) ...<ref name="dbsnp"> Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward and Stephen T. Sherry (2000): "dbSNP: a database of single nucleotide polymorphisms". Nucleic Acids Research Vol.28(1): 352-355. PubMed:10592272 </ref>

SNPdbe

SNPdbe (nsSNP database of functional effects) ... <ref name="snpdbe"> Christian Schaefer, Alice Meier, Burkhard Rost and Yana Bromberg (2012): "SNPdbe: constructing an nsSNP functional impacts database". Bioinformatics Vol.28(4): 601-602. doi:10.1093/bioinformatics/btr705 </ref>

OMIM

OMIM (Online Mendelian Inheritance in Man) is a comprehensive, daily updated and online freely available knowledgebase of human genes and genetic disorders. An entry in OMIM includes the primary and sometimes alternative title and symbol, a gene map locus which displays the cytogenetic location of the gene or disorder, multiple map locations if a disease is known to be genetically heterogeneous, links to the NCBI’s ‘neighboring’ feature and several other informations and links to many useful genetic resources. Within the relevant gene entry allelic variants with functional significance are maintained. A few polymorphisms, associated with particular common disorders, are included as well. OMIM is particularly easy and uncomplicated for the use of the growing information in human genetics. The information is derived from biomedical literature and is written and edited at the John Hopkins University with input from scientists and physicians all over the world. <ref name="omim"> Ada Hamosh, Alan F Scott, Joanna S Amberger, Carol A Bocchini and Victor A McKusick (2005): "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders". Nucleic Acids Research Vol.33 (Database issue): D514-D517. doi:10.1093/nar/gki033, PubMed:15608251</ref>

SNPedia

SNPedia is a wiki resource, which ... <ref name="snpedia"> Michael Cariaso and Greg Lennon (2012): "SNPedia: a wiki supporting personal genome annotation, interpretation and analysis". Nucleic Acids Research Vol.40 (Database issue): D1308-D1312. doi:10.1093/nar/gkr798 </ref>

Mutation Map

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References

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