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 ENST00000394120
Genbank transcript ID NM_001130455
UniProt peptide O75923
alteration type single base exchange
alteration region CDS
DNA changes c.3140G>A
cDNA.3281G>A
g.116983G>A
AA changes R1047H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1047
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      1047YTHRRRRWVRLRRRDLSQMEALKR
mutated  not conserved    1047YTHRRRRWVRLHRRDLSQMEALK
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 6246 / 6246
position (AA) of stopcodon in wt / mu AA sequence 2082 / 2082
position of stopcodon in wt / mu cDNA 6387 / 6387
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 142 / 142
chromosome 2
strand 1
last intron/exon boundary 6349
theoretical NMD boundary in CDS 6157
length of CDS 6246
coding sequence (CDS) position 3140
cDNA position
(for ins/del: last normal base / first normal base)		 3281
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 MLCCLLVRAS NLPSAKKDRR SDPVASLTFR GVKKRTKVIK NSVNPVWNEG FEWDLKGIPL
DQGSELHVVV KDHETMGRNR FLGEAKVPLR EVLATPSLSA SFNAPLLDTK KQPTGASLVL
QVSYTPLPGA VPLFPPPTPL EPSPTLPDLD VVADTGGEED TEDQGLTGDE AEPFLDQSGG
PGAPTTPRKL PSRPPPHYPG IKRKRSAPTS RKLLSDKPQD FQIRVQVIEG RQLPGVNIKP
VVKVTAAGQT KRTRIHKGNS PLFNETLFFN LFDSPGELFD EPIFITVVDS RSLRTDALLG
EFRMDVGTIY REPRHAYLRK WLLLSDPDDF SAGARGYLKT SLCVLGPGDE APLERKDPSE
DKEDIESNLL RPTGVALRGA HFCLKVFRAE DLPQMDDAVM DNVKQIFGFE SNKKNLVDPF
VEVSFAGKML CSKILEKTAN PQWNQNITLP AMFPSMCEKM RIRIIDWDRL THNDIVATTY
LSMSKISAPG GEIEEEPAGA VKPSKASDLD DYLGFLPTFG PCYINLYGSP REFTGFPDPY
TELNTGKGEG VAYRGRLLLS LETKLVEHSE QKVEDLPADD ILRVEKYLRR RKYSLFAAFY
SATMLQDVDD AIQFEVSIGN YGNKFDMTCL PLASTTQYSR AVFDGCHYYY LPWGNVKPVV
VLSSYWEDIS HRIETQNQLL GIADRLEAGL EQVHLALKAQ CSTEDVDSLV AQLTDELIAG
CSQPLGDIHE TPSATHLDQY LYQLRTHHLS QITEAALALK LGHSELPAAL EQAEDWLLRL
RALAEEPQNS LPDIVIWMLQ GDKRVAYQRV PAHQVLFSRR GANYCGKNCG KLQTIFLKYP
MEKVPGARMP VQIRVKLWFG LSVDEKEFNQ FAEGKLSVFA ETYENETKLA LVGNWGTTGL
TYPKFSDVTG KIKLPKDSFR PSAGWTWAGD WFVCPEKTLL HDMDAGHLSF VEEVFENQTR
LPGGQWIYMS DNYTDVNGEK VLPKDDIECP LGWKWEDEEW STDLNRAVDE QGWEYSITIP
PERKPKHWVP AEKMYYTHRR RRWVRLRRRD LSQMEALKRH RQAEAEGEGW EYASLFGWKF
HLEYRKTDAF RRRRWRRRME PLEKTGPAAV FALEGALGGV MDDKSEDSMS VSTLSFGVNR
PTISCIFDYG NRYHLRCYMY QARDLAAMDK DSFSDPYAIV SFLHQSQKTV VVKNTLNPTW
DQTLIFYEIE IFGEPATVAE QPPSIVVELY DHDTYGADEF MGRCICQPSL ERMPRLAWFP
LTRGSQPSGE LLASFELIQR EKPAIHHIPG FEVQETSRIL DESEDTDLPY PPPQREANIY
MVPQNIKPAL QRTAIEILAW GLRNMKSYQL ANISSPSLVV ECGGQTVQSC VIRNLRKNPN
FDICTLFMEV MLPREELYCP PITVKVIDNR QFGRRPVVGQ CTIRSLESFL CDPYSAESPS
PQGGPDDVSL LSPGEDVLID IDDKEPLIPI QEEEFIDWWS KFFASIGERE KCGSYLEKDF
DTLKVYDTQL ENVEAFEGLS DFCNTFKLYR GKTQEETEDP SVIGEFKGLF KIYPLPEDPA
IPMPPRQFHQ LAAQGPQECL VRIYIVRAFG LQPKDPNGKC DPYIKISIGK KSVSDQDNYI
PCTLEPVFGK MFELTCTLPL EKDLKITLYD YDLLSKDEKI GETVVDLENR LLSKFGARCG
LPQTYCVSGP NQWRDQLRPS QLLHLFCQQH RVKAPVYRTD RVMFQDKEYS IEEIEAGRIP
NPHLGPVEER LALHVLQQQG LVPEHVESRP LYSPLQPDIE QGKLQMWVDL FPKALGRPGP
PFNITPRRAR RFFLRCIIWN TRDVILDDLS LTGEKMSDIY VKGWMIGFEE HKQKTDVHYR
SLGGEGNFNW RFIFPFDYLP AEQVCTIAKK DAFWRLDKTE SKIPARVVFQ IWDNDKFSFD
DFLGSLQLDL NRMPKPAKTA KKCSLDQLDD AFHPEWFVSL FEQKTVKGWW PCVAEEGEKK
ILAGKLEMTL EIVAESEHEE RPAGQGRDEP NMNPKLEDPR RPDTSFLWFT SPYKTMKFIL
WRRFRWAIIL FIILFILLLF LAIFIYAFPN YAAMKLVKPF S*
mutated AA sequence MLCCLLVRAS NLPSAKKDRR SDPVASLTFR GVKKRTKVIK NSVNPVWNEG FEWDLKGIPL
DQGSELHVVV KDHETMGRNR FLGEAKVPLR EVLATPSLSA SFNAPLLDTK KQPTGASLVL
QVSYTPLPGA VPLFPPPTPL EPSPTLPDLD VVADTGGEED TEDQGLTGDE AEPFLDQSGG
PGAPTTPRKL PSRPPPHYPG IKRKRSAPTS RKLLSDKPQD FQIRVQVIEG RQLPGVNIKP
VVKVTAAGQT KRTRIHKGNS PLFNETLFFN LFDSPGELFD EPIFITVVDS RSLRTDALLG
EFRMDVGTIY REPRHAYLRK WLLLSDPDDF SAGARGYLKT SLCVLGPGDE APLERKDPSE
DKEDIESNLL RPTGVALRGA HFCLKVFRAE DLPQMDDAVM DNVKQIFGFE SNKKNLVDPF
VEVSFAGKML CSKILEKTAN PQWNQNITLP AMFPSMCEKM RIRIIDWDRL THNDIVATTY
LSMSKISAPG GEIEEEPAGA VKPSKASDLD DYLGFLPTFG PCYINLYGSP REFTGFPDPY
TELNTGKGEG VAYRGRLLLS LETKLVEHSE QKVEDLPADD ILRVEKYLRR RKYSLFAAFY
SATMLQDVDD AIQFEVSIGN YGNKFDMTCL PLASTTQYSR AVFDGCHYYY LPWGNVKPVV
VLSSYWEDIS HRIETQNQLL GIADRLEAGL EQVHLALKAQ CSTEDVDSLV AQLTDELIAG
CSQPLGDIHE TPSATHLDQY LYQLRTHHLS QITEAALALK LGHSELPAAL EQAEDWLLRL
RALAEEPQNS LPDIVIWMLQ GDKRVAYQRV PAHQVLFSRR GANYCGKNCG KLQTIFLKYP
MEKVPGARMP VQIRVKLWFG LSVDEKEFNQ FAEGKLSVFA ETYENETKLA LVGNWGTTGL
TYPKFSDVTG KIKLPKDSFR PSAGWTWAGD WFVCPEKTLL HDMDAGHLSF VEEVFENQTR
LPGGQWIYMS DNYTDVNGEK VLPKDDIECP LGWKWEDEEW STDLNRAVDE QGWEYSITIP
PERKPKHWVP AEKMYYTHRR RRWVRLHRRD LSQMEALKRH RQAEAEGEGW EYASLFGWKF
HLEYRKTDAF RRRRWRRRME PLEKTGPAAV FALEGALGGV MDDKSEDSMS VSTLSFGVNR
PTISCIFDYG NRYHLRCYMY QARDLAAMDK DSFSDPYAIV SFLHQSQKTV VVKNTLNPTW
DQTLIFYEIE IFGEPATVAE QPPSIVVELY DHDTYGADEF MGRCICQPSL ERMPRLAWFP
LTRGSQPSGE LLASFELIQR EKPAIHHIPG FEVQETSRIL DESEDTDLPY PPPQREANIY
MVPQNIKPAL QRTAIEILAW GLRNMKSYQL ANISSPSLVV ECGGQTVQSC VIRNLRKNPN
FDICTLFMEV MLPREELYCP PITVKVIDNR QFGRRPVVGQ CTIRSLESFL CDPYSAESPS
PQGGPDDVSL LSPGEDVLID IDDKEPLIPI QEEEFIDWWS KFFASIGERE KCGSYLEKDF
DTLKVYDTQL ENVEAFEGLS DFCNTFKLYR GKTQEETEDP SVIGEFKGLF KIYPLPEDPA
IPMPPRQFHQ LAAQGPQECL VRIYIVRAFG LQPKDPNGKC DPYIKISIGK KSVSDQDNYI
PCTLEPVFGK MFELTCTLPL EKDLKITLYD YDLLSKDEKI GETVVDLENR LLSKFGARCG
LPQTYCVSGP NQWRDQLRPS QLLHLFCQQH RVKAPVYRTD RVMFQDKEYS IEEIEAGRIP
NPHLGPVEER LALHVLQQQG LVPEHVESRP LYSPLQPDIE QGKLQMWVDL FPKALGRPGP
PFNITPRRAR RFFLRCIIWN TRDVILDDLS LTGEKMSDIY VKGWMIGFEE HKQKTDVHYR
SLGGEGNFNW RFIFPFDYLP AEQVCTIAKK DAFWRLDKTE SKIPARVVFQ IWDNDKFSFD
DFLGSLQLDL NRMPKPAKTA KKCSLDQLDD AFHPEWFVSL FEQKTVKGWW PCVAEEGEKK
ILAGKLEMTL EIVAESEHEE RPAGQGRDEP NMNPKLEDPR RPDTSFLWFT SPYKTMKFIL
WRRFRWAIIL FIILFILLLF LAIFIYAFPN YAAMKLVKPF S*
speed 1.01 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