Researching SNPs Gaucher Disease

The aim of this task was to map non-synonymous SNPs known for the Gaucher Disease causing gene GBA onto the corresponding protein sequence P04062. Several databases should be taken into account, namely HGMD<ref name="hgmd">Stenson et al. (2009). The Human Gene Mutation Database (HGMD): 2008 Update. Genome Med</ref>, dbSNP<ref name="dbsnp">Sherry ST, Ward M, and Sirotkin, K. (1999). dbSNP - database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Research</ref>, SNPdb <ref name="snpdbe">C Schaefer, A Meier, B Rost. (2012). SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics</ref>, and OMIN <ref name="omim">Hamosh, A.; Scott, A.; Amberger, J.; Bocchini, C.; McKusick, V. (2004). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research</ref>. Technical details are reported in our protocol.

HGMD

The Human Genome Mutation Database (HGMD) is a collection of observed mutations in the human genome which are associated with various diseases. The mutations are taken from publications, both manually and automatically [1]. There is a public version with 88745 entries (9th June, 2012) and a professional version with 123565 entries. Since 2009, the public version has been extended only by few new entries such that it does no longer contain all currently known mutations [2]. The HGMD encompasses following types of mutations:

Missense

Mutations which result in another amino acid

Nonsense

Mutations which result in a stop codon

Splicing

Mutations which alter splice sites

Regulatory

Mutation which alter gene regulation

Small/gross deletions

Deletions which remove residues

Small/gross insertions

Insertions which give rise to new residues

Small indels

Insertions or deletions

Duplications

Duplication of gene fragments

Complex rearrangements

Change in the location for gene fragments

Repeat variations

Varying number of sequence copies

<xr id="tab:hgmd_number"/> lists the number of mutations annotated in HGMD for GBA. A comprehensive list of all missense/nonsense mutations can be obtained by following the respective hyperlink.

<figtable id="tab:hgmd_number">

Type	Count
Missense/nonsense	250
Splicing	15
Regulatory	0
Small deletions	26
Small insertions	13
Small indels	2
Gross deletions	3
Gross insertions/duplications	1
Complex rearrangements	15
Public total	325

Number of mutations in HGMD for GBA. </figtable>

<xr id="tab:hgmd_map"/> shows the wildtype version of P04062 with non-synonymous mutations highlighted in red. Since the transcript NM_001005741.1 already referred to P04062, the amino acid positions could be used directly for creating <xr id="tab:hgmd_map"/> without any additional translation.

<figtable id="tab:hgmd_map">

               1          11         21         31         41         51         61         71        
Wildtype       MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT YCDSFDPPTF PALGTFSRYE
Non-synonymous MEFSSPSREE CPRPLSRVSI MAGSLTGLLL LQAVS!ASGA RPCIPKSFSY ISVLSVCNAT YCNSFDPPTF PALSTVSRYK
               81         91         101        111        121        131        141        151       
Wildtype       STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV
Non-synonymous NIRSE!QMEL SMGPIQANHT GTGLPLTLQP E!!FQKANGF GGATTDAATL NILALSPPAQ NLLRKLCVSK EEIGYDISQA
               161        171        181        191        201        211        221        231       
Wildtype       PMASCDFSIR TYTYADTPDD FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
Non-synonymous LVASCVFSIL TYP!EDTPHD FQLHNFSLPE ADTKLQILLS PQALQLA!CP V!PLDSS!PS LTRFKTKVEG NGKWPPEGQP
               241        251        261        271        281        291        301        311       
Wildtype       GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA RDLGPTLANS THHNVRLLML
Non-synonymous EDICHQTRVR HCVKYLDACA EHKLQFWAVR A!NETPAVLL SVHHFQCQGL TPEQQ!DLTA HDLDATLANG THHNVRLPML
               321        331        341        351        361        371        381        391       
Wildtype       DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM
Non-synonymous DDQHLLPLHW AKVVLTDPEA AI!LHGIVVR RHLHFLDSAK AIPWKTHCLS PNTMPFASET YVGSKFGK!S LWLDF!D!GI
               401        411        421        431        441        451        461        471       
Wildtype       QYSHSIITNL LYHVVGWTDW NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
Non-synonymous QCRHGIIMKV LYHLVS!TA! KRDPNL!ERL IRLCTSFYSL FIVDITKHTI HQRRVVCHLD HFSEVIPEGS QGVGLVASQK
               481        491        501        511        521        531       
Wildtype       NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ
Non-synonymous NDRDPVALMR PDGSPVVVMP KPSSKDVPLT IKYPAVSFPE TISPGYPTHI YLWRCR

Genetic variants of P04062 annotated in HGMD. Red: non-synonymous mutations; </figtable>

<figure id="fig:hgmd_2nt0_A">

Genetic variants of P04062 annotated in HGMD mapped to 2nt0_A. Red: non-synonymous mutations

</figure>

In order to get an expression about the structural elements which are subject to mutations, we mapped the mutations of <xr id="tab:hgmd_map"/> from P04062 to its closest crystal structure 2nt0. We found that the mutations were scattered all over the structure without major aggregations in certain domains (cf. <xr id="fig:hgmd_2nt0_A"/>).

dbSNP

dbSNP is a publicly available collection of genetic variations from different species. Genetic variations include (1) SNPs, (2) short deletion and insertion polymorphisms (indels/DIPs), (3) microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, and (6) named variants. Genetic variants are submitted by, amongst others, research institutions, large scale genome sequencing centers, and other SNP databases. Statistics about the latest release can be found here.

Variations of GBA in dbSNP included 92 missense mutations, 47 synonymous mutations and 3 deletions. Missense and synonymous mutations are visualized in <xr id="tab:dbsnp_map"/>. All three deletions cause a frame-shift due to the loss of a single nucleotide which severely alters the amino acid sequence after the position where the mutation occurred. The effect would be less severe if a complete codon were inserted or deleted which would change the length of the protein sequence but not the amino acid composition.

<figtable id="tab:dbsnp_map">

               1          11         21         31         41         51         61         71        
Wildtype       MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT YCDSFDPPTF PALGTFSRYE
Non-synonymous MEFSSPSREE CPRPSGGVSV MAGSLTGLLL LQAVSWASGA CPCIPESFGY SSVVCVCNAT YYESFDPRTF PALGTLSCYK
Synonymous     MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT YCDSFDPPTF PALGTFSRYE
               81         91         101        111        121        131        141        151       
Wildtype       STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV
Non-synonymous SRSSGQWMEL STGPIQANYT GTGLLLTLQP EQKFQKVKGF GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYKISWV
Synonymous     STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV
               161        171        181        191        201        211        221        231       
Wildtype       PMASCDFSIR TYTYADTPDD FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
Non-synonymous LIASCVFSIL TYIYEDTPHD FQLHNFSLPE EDTKLNILLN PRALQLAQRP ISLLASPWTS LTRLKTKVEE NGKESLKGQP
Synonymous     PMASCDFSIR TYTYADTPDD FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
               241        251        261        271        281        291        301        311       
Wildtype       GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA RDLGPTLANS THHNVRLLML
Non-synonymous EDICHQTWAR YLVKFLDAYA EHKLQFWAVR AENEPSAGLL NGYPFQCLGF TPEHQRDFIA HDLDRTLANG THHNVRLLML
Synonymous     GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA RDLGPTLANS THHNVRLLML
               321        331        341        351        361        371        381        391       
Wildtype       DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM
Non-synonymous DDQHLLLPQW AKVVLTDPEA AICVYGIAVH WYLDFLDPAK ATLGETHHLF PNTMLFASEA CVGSKFWEQS VQLGSWDQGI
Synonymous     DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM
               401        411        421        431        441        451        461        471       
Wildtype       QYSHSIITNL LYHVVGWTDW NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
Non-synonymous QCSHRIIMNL LYHVVGCTAW NIALNPKGGL IWVRTSVESP TIVDITKETL YKQPILCHLG HFSKFIPEGS QRVGLVASPK
Synonymous     QYSHSIITNL LYHVVGWTDW NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
               481        491        501        511        521        531       
Wildtype       NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ
Non-synonymous NNLDAVALMR PDGSAVVVVL NRSFKDVPPT IKEPAVGFLE TISPGYSIHI YLWCHQ
Synonymous     NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ

Genetic variants of P04062 annotated in dbSNP. Red: missense mutations; Green: synonymous mutations; Purple: missense and synonymous mutations. </figtable>

</figure> </figure>

Genetic variants of P04062 annotated in dbSNP mapped to 2nt0_A. Red: missense mutations; Green: synonymous mutations; Purple: missense and synonymous mutations.

Overlap of non-synonymous mutations between HGMD and dbSNP.

<figure id="fig:dbsnp_2nt0_A">

<figure id="fig:hgmd_dbsnp">

<xr id="fig:dbsnp_2nt0_A"/> visualises the genetic variants of <xr id="tab:dbsnp_map"/> in 2nt0_A. As in <xr id="fig:hgmd_2nt0_A"/>, the mutations were evenly distributed with a slightly higher concentration in the glycosyl hydrolase domain (the domain on the left hand site).

<xr id="fig:hgmd_dbsnp"/> depicts the overlap of non-synonymous mutations between HGMD and dbSNP. If shows that HGMD comprises significantly more non-synonymous mutations than dbSNP although it has not been updated since 2009.

SNPdbe

SNPdbe (nsSNP database of functional effects) is a database and a web interface which provides predictions of computationally annotated functional impacts of SNPs. Instead of SNPs, each entry is represented as a SAAS (single amino acid substitution) which means each non-synonymous SNP (nsSNP) changes one amino acid in the gene product. The impact of SAAS is predicted by using the SNAP and SIFT algorithms and is augmented with the information and disease associations from PMD, OMIM and UniProt. In the up to date version (2012/03/05), SNPdbe contains 1691464 entries/SAASs which belong to 2985 Organisms and 159142 Protein sequences.

We tried to search the gene symbol(GBA), protein (UniProt) id(P04062), and the disease name (gaucher), different number of SNPs were returned (GBA: 563, p04062: 163, gaucher: 174). The results were all mixed with the SAASs located at similar protein sequences from different database (e.g. NCBI or UniProt).

The searching results which were only limited to the protein seqeunce p04062 returns 65 SAASs, in red color as showing in the following map. All of them have no experimental evidence. The SAASs with high conservation score (which showed that is a mutant more than a wildtype) are labeled in blue :

<figtable id="tab:snpdbe_map">

SAASs    NDRDPVALMH PDGSAVLVVP KPSSKDVPLT IKYPAVGFLE TISPGYSIHT YLWRCQ
         1          11         21         31         41         51         61         71        
Wildtype MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT YCDSFDPPTF PALGTFSRYE
SAASs    MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVSVCNAT YCNSFDPPTF PALGTVSRYE
         81         91         101        111        121        131        141        151       
Wildtype STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV
SAASs    STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF GGAMTDAATL NILALSPPAQ NLLLKLYFSE EEIGYDITRV
         161        171        181        191        201        211        221        231       
Wildtype PMASCDFSIR TYTYADTPDD FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
SAASs    PVASCDFSIC TYPYADTPDD FQLHNFSLPE EDTKLKITLI HRALQLAQPP VSFLDSSWTS TTWFKTNGTV NEKWSLEGQP
         241        251        261        271        281        291        301        311       
Wildtype GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA RDLGPTLANS THHNVRLLML
SAASs    RDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPPAGLL SGYPFQCLGF TPEQQRDLIA RDIGPTLANS THHNVRLLML
         321        331        341        351        361        371        381        391       
Wildtype DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM
SAASs    DDQCLLLPHW AKVVLTDPEA AKYVHGIAVH WHLHFLAPAK ATPGETHRLF PNTMLFASET CVGSKFWKQS LWLGSWDRGM
         401        411        421        431        441        451        461        471       
Wildtype QYSHSIITNL LYHVVGWTDW NLALNPENGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
SAASs    QYSHNIITNL LYHLVGGTHW KLALNLEERP NRVRNFLNSP FIVDITKDTI HQQPVVYHLD HFSEFIPEGS QRVGLVASQK
         481        491        501        511        521        531       
Wildtype NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ
SAASs    NDRDPVALMH PDGSAVLVVP KPSSKDVPLT IKYPAVGFLE TISPGYSIHT YLWRCQ

Genetic variants of P04062 annotated in SNPdbe. Red: missense mutations(SAASs), Blue: SAASs with high conservation score. </figtable>

OMIM

OMIM (Online Mendelian Inheritance in Man) is a database containing information on all known genetic disorders and the corresponding genes in human genome with particular focus on the molecular relationship between phenotype and genotype. In the up to date version (8 June 2012), there are 19971 autosomal related, 1171 X-linked,59 Y-linked, 65 Mitochondrial related entries. Each entry is either Gene description with/without phenotype information, or phenotype description with/without molecular basis.

SNPedia

SNPedia is wiki styled database providing the information about the effects of SNPs. Each entry contains a description of a SNP, together with the links to scientific publications and other related genomics web sites. The SNPs data is supported by some personal genomics company, e.g., 23andMe, Navigenics, deCODEme or Knome. In the up to data version of SNPedia, there are 29135 SNPs.

References

<references/>