Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999930140464966 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM994326)
  • known disease mutation: rs6675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:71797834G>AN/A show variant in all transcripts   IGV
HGNC symbol DYSF
Ensembl transcript ID ENST00000258104
Genbank transcript ID NM_003494
UniProt peptide O75923
alteration type single base exchange
alteration region CDS
DNA changes c.3137G>A
cDNA.3414G>A
g.116983G>A
AA changes R1046H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1046
frameshift no
known variant Reference ID: rs121908958
databasehomozygous (A/A)heterozygousallele carriers
1000G022
ExAC033

known disease mutation: rs6675 (pathogenic for Autosomal recessive limb-girdle muscular dystrophy type 2B|Myopathy, distal, with anterior tibial onset|Qualitative or quantitative defects of dysferlin|Miyoshi muscular dystrophy 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994326)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994326)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994326)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4811
3.7651
(flanking)0.2530.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased116983wt: 0.42 / mu: 0.95wt: CCTGCGCAGGAGGGA
mu: CCTGCACAGGAGGGA		 TGCG|cagg
Donor increased116988wt: 0.69 / mu: 0.77wt: GCAGGAGGGATCTCA
mu: ACAGGAGGGATCTCA		 AGGA|ggga
Donor increased116985wt: 0.73 / mu: 0.83wt: TGCGCAGGAGGGATC
mu: TGCACAGGAGGGATC		 CGCA|ggag
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1046YTHRRRRWVRLRRRDLSQMEALKR
mutated  not conserved    1046YTHRRRRWVRLHRRDLSQMEALK
Ptroglodytes  all identical  ENSPTRG00000012049  1039YTHRRRRWVRLRRR
Mmulatta  all identical  ENSMMUG00000007176  1017YTHRRRRWVRLRRRDLSQMEALK
Fcatus  all identical  ENSFCAG00000004357  1016YTHRRRRWVRLRRR
Mmusculus  all identical  ENSMUSG00000033788  1066YTHRRRRWVRLRRRDLSQMEALK
Ggallus  no alignment  ENSGALG00000016105  n/a
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000007370  809HTNRRRRWIRLRRRDMQKMEALR
Dmelanogaster  no homologue    
Celegans  all identical  T05E8.1  846HNFRKRCIERPRKHE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
12046TOPO_DOMCytoplasmic (Potential).lost
10381097COMPBIASArg-rich.lost
11391244DOMAINC2 4.might get lost (downstream of altered splice site)
15651663DOMAINC2 5.might get lost (downstream of altered splice site)
20472067TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
20682080TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6243 / 6243
position (AA) of stopcodon in wt / mu AA sequence 2081 / 2081
position of stopcodon in wt / mu cDNA 6520 / 6520
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 278 / 278
chromosome 2
strand 1
last intron/exon boundary 6482
theoretical NMD boundary in CDS 6154
length of CDS 6243
coding sequence (CDS) position 3137
cDNA position
(for ins/del: last normal base / first normal base)		 3414
gDNA position
(for ins/del: last normal base / first normal base)		 116983
chromosomal position
(for ins/del: last normal base / first normal base)		 71797834
original gDNA sequence snippet GCGGCGCTGGGTGCGCCTGCGCAGGAGGGATCTCAGCCAAA
altered gDNA sequence snippet GCGGCGCTGGGTGCGCCTGCACAGGAGGGATCTCAGCCAAA
original cDNA sequence snippet GCGGCGCTGGGTGCGCCTGCGCAGGAGGGATCTCAGCCAAA
altered cDNA sequence snippet GCGGCGCTGGGTGCGCCTGCACAGGAGGGATCTCAGCCAAA
wildtype AA sequence MLRVFILYAE NVHTPDTDIS DAYCSAVFAG VKKRTKVIKN SVNPVWNEGF EWDLKGIPLD
QGSELHVVVK DHETMGRNRF LGEAKVPLRE VLATPSLSAS FNAPLLDTKK QPTGASLVLQ
VSYTPLPGAV PLFPPPTPLE PSPTLPDLDV VADTGGEEDT EDQGLTGDEA EPFLDQSGGP
GAPTTPRKLP SRPPPHYPGI KRKRSAPTSR KLLSDKPQDF QIRVQVIEGR QLPGVNIKPV
VKVTAAGQTK RTRIHKGNSP LFNETLFFNL FDSPGELFDE PIFITVVDSR SLRTDALLGE
FRMDVGTIYR EPRHAYLRKW LLLSDPDDFS AGARGYLKTS LCVLGPGDEA PLERKDPSED
KEDIESNLLR PTGVALRGAH FCLKVFRAED LPQMDDAVMD NVKQIFGFES NKKNLVDPFV
EVSFAGKMLC SKILEKTANP QWNQNITLPA MFPSMCEKMR IRIIDWDRLT HNDIVATTYL
SMSKISAPGG EIEEEPAGAV KPSKASDLDD YLGFLPTFGP CYINLYGSPR EFTGFPDPYT
ELNTGKGEGV AYRGRLLLSL ETKLVEHSEQ KVEDLPADDI LRVEKYLRRR KYSLFAAFYS
ATMLQDVDDA IQFEVSIGNY GNKFDMTCLP LASTTQYSRA VFDGCHYYYL PWGNVKPVVV
LSSYWEDISH RIETQNQLLG IADRLEAGLE QVHLALKAQC STEDVDSLVA QLTDELIAGC
SQPLGDIHET PSATHLDQYL YQLRTHHLSQ ITEAALALKL GHSELPAALE QAEDWLLRLR
ALAEEPQNSL PDIVIWMLQG DKRVAYQRVP AHQVLFSRRG ANYCGKNCGK LQTIFLKYPM
EKVPGARMPV QIRVKLWFGL SVDEKEFNQF AEGKLSVFAE TYENETKLAL VGNWGTTGLT
YPKFSDVTGK IKLPKDSFRP SAGWTWAGDW FVCPEKTLLH DMDAGHLSFV EEVFENQTRL
PGGQWIYMSD NYTDVNGEKV LPKDDIECPL GWKWEDEEWS TDLNRAVDEQ GWEYSITIPP
ERKPKHWVPA EKMYYTHRRR RWVRLRRRDL SQMEALKRHR QAEAEGEGWE YASLFGWKFH
LEYRKTDAFR RRRWRRRMEP LEKTGPAAVF ALEGALGGVM DDKSEDSMSV STLSFGVNRP
TISCIFDYGN RYHLRCYMYQ ARDLAAMDKD SFSDPYAIVS FLHQSQKTVV VKNTLNPTWD
QTLIFYEIEI FGEPATVAEQ PPSIVVELYD HDTYGADEFM GRCICQPSLE RMPRLAWFPL
TRGSQPSGEL LASFELIQRE KPAIHHIPGF EVQETSRILD ESEDTDLPYP PPQREANIYM
VPQNIKPALQ RTAIEILAWG LRNMKSYQLA NISSPSLVVE CGGQTVQSCV IRNLRKNPNF
DICTLFMEVM LPREELYCPP ITVKVIDNRQ FGRRPVVGQC TIRSLESFLC DPYSAESPSP
QGGPDDVSLL SPGEDVLIDI DDKEPLIPIQ EEEFIDWWSK FFASIGEREK CGSYLEKDFD
TLKVYDTQLE NVEAFEGLSD FCNTFKLYRG KTQEETEDPS VIGEFKGLFK IYPLPEDPAI
PMPPRQFHQL AAQGPQECLV RIYIVRAFGL QPKDPNGKCD PYIKISIGKK SVSDQDNYIP
CTLEPVFGKM FELTCTLPLE KDLKITLYDY DLLSKDEKIG ETVVDLENRL LSKFGARCGL
PQTYCVSGPN QWRDQLRPSQ LLHLFCQQHR VKAPVYRTDR VMFQDKEYSI EEIEAGRIPN
PHLGPVEERL ALHVLQQQGL VPEHVESRPL YSPLQPDIEQ GKLQMWVDLF PKALGRPGPP
FNITPRRARR FFLRCIIWNT RDVILDDLSL TGEKMSDIYV KGWMIGFEEH KQKTDVHYRS
LGGEGNFNWR FIFPFDYLPA EQVCTIAKKD AFWRLDKTES KIPARVVFQI WDNDKFSFDD
FLGSLQLDLN RMPKPAKTAK KCSLDQLDDA FHPEWFVSLF EQKTVKGWWP CVAEEGEKKI
LAGKLEMTLE IVAESEHEER PAGQGRDEPN MNPKLEDPRR PDTSFLWFTS PYKTMKFILW
RRFRWAIILF IILFILLLFL AIFIYAFPNY AAMKLVKPFS *
mutated AA sequence MLRVFILYAE NVHTPDTDIS DAYCSAVFAG VKKRTKVIKN SVNPVWNEGF EWDLKGIPLD
QGSELHVVVK DHETMGRNRF LGEAKVPLRE VLATPSLSAS FNAPLLDTKK QPTGASLVLQ
VSYTPLPGAV PLFPPPTPLE PSPTLPDLDV VADTGGEEDT EDQGLTGDEA EPFLDQSGGP
GAPTTPRKLP SRPPPHYPGI KRKRSAPTSR KLLSDKPQDF QIRVQVIEGR QLPGVNIKPV
VKVTAAGQTK RTRIHKGNSP LFNETLFFNL FDSPGELFDE PIFITVVDSR SLRTDALLGE
FRMDVGTIYR EPRHAYLRKW LLLSDPDDFS AGARGYLKTS LCVLGPGDEA PLERKDPSED
KEDIESNLLR PTGVALRGAH FCLKVFRAED LPQMDDAVMD NVKQIFGFES NKKNLVDPFV
EVSFAGKMLC SKILEKTANP QWNQNITLPA MFPSMCEKMR IRIIDWDRLT HNDIVATTYL
SMSKISAPGG EIEEEPAGAV KPSKASDLDD YLGFLPTFGP CYINLYGSPR EFTGFPDPYT
ELNTGKGEGV AYRGRLLLSL ETKLVEHSEQ KVEDLPADDI LRVEKYLRRR KYSLFAAFYS
ATMLQDVDDA IQFEVSIGNY GNKFDMTCLP LASTTQYSRA VFDGCHYYYL PWGNVKPVVV
LSSYWEDISH RIETQNQLLG IADRLEAGLE QVHLALKAQC STEDVDSLVA QLTDELIAGC
SQPLGDIHET PSATHLDQYL YQLRTHHLSQ ITEAALALKL GHSELPAALE QAEDWLLRLR
ALAEEPQNSL PDIVIWMLQG DKRVAYQRVP AHQVLFSRRG ANYCGKNCGK LQTIFLKYPM
EKVPGARMPV QIRVKLWFGL SVDEKEFNQF AEGKLSVFAE TYENETKLAL VGNWGTTGLT
YPKFSDVTGK IKLPKDSFRP SAGWTWAGDW FVCPEKTLLH DMDAGHLSFV EEVFENQTRL
PGGQWIYMSD NYTDVNGEKV LPKDDIECPL GWKWEDEEWS TDLNRAVDEQ GWEYSITIPP
ERKPKHWVPA EKMYYTHRRR RWVRLHRRDL SQMEALKRHR QAEAEGEGWE YASLFGWKFH
LEYRKTDAFR RRRWRRRMEP LEKTGPAAVF ALEGALGGVM DDKSEDSMSV STLSFGVNRP
TISCIFDYGN RYHLRCYMYQ ARDLAAMDKD SFSDPYAIVS FLHQSQKTVV VKNTLNPTWD
QTLIFYEIEI FGEPATVAEQ PPSIVVELYD HDTYGADEFM GRCICQPSLE RMPRLAWFPL
TRGSQPSGEL LASFELIQRE KPAIHHIPGF EVQETSRILD ESEDTDLPYP PPQREANIYM
VPQNIKPALQ RTAIEILAWG LRNMKSYQLA NISSPSLVVE CGGQTVQSCV IRNLRKNPNF
DICTLFMEVM LPREELYCPP ITVKVIDNRQ FGRRPVVGQC TIRSLESFLC DPYSAESPSP
QGGPDDVSLL SPGEDVLIDI DDKEPLIPIQ EEEFIDWWSK FFASIGEREK CGSYLEKDFD
TLKVYDTQLE NVEAFEGLSD FCNTFKLYRG KTQEETEDPS VIGEFKGLFK IYPLPEDPAI
PMPPRQFHQL AAQGPQECLV RIYIVRAFGL QPKDPNGKCD PYIKISIGKK SVSDQDNYIP
CTLEPVFGKM FELTCTLPLE KDLKITLYDY DLLSKDEKIG ETVVDLENRL LSKFGARCGL
PQTYCVSGPN QWRDQLRPSQ LLHLFCQQHR VKAPVYRTDR VMFQDKEYSI EEIEAGRIPN
PHLGPVEERL ALHVLQQQGL VPEHVESRPL YSPLQPDIEQ GKLQMWVDLF PKALGRPGPP
FNITPRRARR FFLRCIIWNT RDVILDDLSL TGEKMSDIYV KGWMIGFEEH KQKTDVHYRS
LGGEGNFNWR FIFPFDYLPA EQVCTIAKKD AFWRLDKTES KIPARVVFQI WDNDKFSFDD
FLGSLQLDLN RMPKPAKTAK KCSLDQLDDA FHPEWFVSLF EQKTVKGWWP CVAEEGEKKI
LAGKLEMTLE IVAESEHEER PAGQGRDEPN MNPKLEDPRR PDTSFLWFTS PYKTMKFILW
RRFRWAIILF IILFILLLFL AIFIYAFPNY AAMKLVKPFS *
speed 1.08 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project