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 ENST00000410020
Genbank transcript ID NM_001130987
UniProt peptide O75923
alteration type single base exchange
alteration region CDS
DNA changes c.3191G>A
cDNA.3332G>A
g.116983G>A
AA changes R1064H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1064
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      1064YTHRRRRWVRLRRRDLSQMEALKR
mutated  not conserved    1064YTHRRRRWVRLHRRDLSQMEALK
Ptroglodytes  all identical  ENSPTRG00000012049  1039YTHRRRRWVRLRRR
Mmulatta  all identical  ENSMMUG00000007176  1017YTHRRRRWVRLRRRDLSQMEALK
Fcatus  all identical  ENSFCAG00000004357  1016YTHRRRRWVRLRRRDLSQMEALK
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  839HNFRKRCIERPRKHE
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 6360 / 6360
position (AA) of stopcodon in wt / mu AA sequence 2120 / 2120
position of stopcodon in wt / mu cDNA 6501 / 6501
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 6463
theoretical NMD boundary in CDS 6271
length of CDS 6360
coding sequence (CDS) position 3191
cDNA position
(for ins/del: last normal base / first normal base)		 3332
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 VVAGGGQSRA ETWSLLSDST MDTRYSGKKW
PAPTDTGGEE DTEDQGLTGD EAEPFLDQSG GPGAPTTPRK LPSRPPPHYP GIKRKRSAPT
SRKLLSDKPQ DFQIRVQVIE GRQLPGVNIK PVVKVTAAGQ TKRTRIHKGN SPLFNETLFF
NLFDSPGELF DEPIFITVVD SRSLRTDALL GEFRMDVGTI YREPRHAYLR KWLLLSDPDD
FSAGARGYLK TSLCVLGPGD EAPLERKDPS EDKEDIESNL LRPTGVALRG AHFCLKVFRA
EDLPQMDDAV MDNVKQIFGF ESNKKNLVDP FVEVSFAGKM LCSKILEKTA NPQWNQNITL
PAMFPSMCEK MRIRIIDWDR LTHNDIVATT YLSMSKISAP GGEIEVDDYL GFLPTFGPCY
INLYGSPREF TGFPDPYTEL NTGKGEGVAY RGRLLLSLET KLVEHSEQKV EDLPADDILR
VEKYLRRRKY SLFAAFYSAT MLQDVDDAIQ FEVSIGNYGN KFDMTCLPLA STTQYSRAVF
DGCHYYYLPW GNVKPVVVLS SYWEDISHRI ETQNQLLGIA DRLEAGLEQV HLALKAQCST
EDVDSLVAQL TDELIAGCSQ PLGDIHETPS ATHLDQYLYQ LRTHHLSQIT EAALALKLGH
SELPAALEQA EDWLLRLRAL AEEPQNSLPD IVIWMLQGDK RVAYQRVPAH QVLFSRRGAN
YCGKNCGKLQ TIFLKYPMEK VPGARMPVQI RVKLWFGLSV DEKEFNQFAE GKLSVFAETY
ENETKLALVG NWGTTGLTYP KFSDVTGKIK LPKDSFRPSA GWTWAGDWFV CPEKTLLHDM
DAGHLSFVEE VFENQTRLPG GQWIYMSDNY TDVNGEKVLP KDDIECPLGW KWEDEEWSTD
LNRAVDEQGW EYSITIPPER KPKHWVPAEK MYYTHRRRRW VRLRRRDLSQ MEALKRHRQA
EAEGEGWEYA SLFGWKFHLE YRKTDAFRRR RWRRRMEPLE KTGPAAVFAL EGALGGVMDD
KSEDSMSVST LSFGVNRPTI SCIFDYGNRY HLRCYMYQAR DLAAMDKDSF SDPYAIVSFL
HQSQKTVVVK NTLNPTWDQT LIFYEIEIFG EPATVAEQPP SIVVELYDHD TYGADEFMGR
CICQPSLERM PRLAWFPLTR GSQPSGELLA SFELIQREKP AIHHIPGFEV QETSRILDES
EDTDLPYPPP QREANIYMVP QNIKPALQRT AIEILAWGLR NMKSYQLANI SSPSLVVECG
GQTVQSCVIR NLRKNPNFDI CTLFMEVMLP REELYCPPIT VKVIDNRQFG RRPVVGQCTI
RSLESFLCDP YSAESPSPQG GPDDVSLLSP GEDVLIDIDD KEPLIPIQLA DGLSSLAPTN
TASPPSSPHE EEFIDWWSKF FASIGEREKC GSYLEKDFDT LKVYDTQLEN VEAFEGLSDF
CNTFKLYRGK TQEETEDPSV IGEFKGLFKI YPLPEDPAIP MPPRQFHQLA AQGPQECLVR
IYIVRAFGLQ PKDPNGKCDP YIKISIGKKS VSDQDNYIPC TLEPVFGKMF ELTCTLPLEK
DLKITLYDYD LLSKDEKIGE TVVDLENRLL SKFGARCGLP QTYCVSGPNQ WRDQLRPSQL
LHLFCQQHRV KAPVYRTDRV MFQDKEYSIE EIEAGRIPNP HLGPVEERLA LHVLQQQGLV
PEHVESRPLY SPLQPDIEQG KLQMWVDLFP KALGRPGPPF NITPRRARRF FLRCIIWNTR
DVILDDLSLT GEKMSDIYVK GWMIGFEEHK QKTDVHYRSL GGEGNFNWRF IFPFDYLPAE
QVCTIAKKDA FWRLDKTESK IPARVVFQIW DNDKFSFDDF LGSLQLDLNR MPKPAKTAKK
CSLDQLDDAF HPEWFVSLFE QKTVKGWWPC VAEEGEKKIL AGKLEMTLEI VAESEHEERP
AGQGRDEPNM NPKLEDPRRP DTSFLWFTSP YKTMKFILWR RFRWAIILFI ILFILLLFLA
IFIYAFPNYA AMKLVKPFS*
mutated AA sequence MLCCLLVRAS NLPSAKKDRR SDPVASLTFR GVKKRTKVIK NSVNPVWNEG FEWDLKGIPL
DQGSELHVVV KDHETMGRNR FLGEAKVPLR EVLATPSLSA SFNAPLLDTK KQPTGASLVL
QVSYTPLPGA VPLFPPPTPL EPSPTLPDLD VVAGGGQSRA ETWSLLSDST MDTRYSGKKW
PAPTDTGGEE DTEDQGLTGD EAEPFLDQSG GPGAPTTPRK LPSRPPPHYP GIKRKRSAPT
SRKLLSDKPQ DFQIRVQVIE GRQLPGVNIK PVVKVTAAGQ TKRTRIHKGN SPLFNETLFF
NLFDSPGELF DEPIFITVVD SRSLRTDALL GEFRMDVGTI YREPRHAYLR KWLLLSDPDD
FSAGARGYLK TSLCVLGPGD EAPLERKDPS EDKEDIESNL LRPTGVALRG AHFCLKVFRA
EDLPQMDDAV MDNVKQIFGF ESNKKNLVDP FVEVSFAGKM LCSKILEKTA NPQWNQNITL
PAMFPSMCEK MRIRIIDWDR LTHNDIVATT YLSMSKISAP GGEIEVDDYL GFLPTFGPCY
INLYGSPREF TGFPDPYTEL NTGKGEGVAY RGRLLLSLET KLVEHSEQKV EDLPADDILR
VEKYLRRRKY SLFAAFYSAT MLQDVDDAIQ FEVSIGNYGN KFDMTCLPLA STTQYSRAVF
DGCHYYYLPW GNVKPVVVLS SYWEDISHRI ETQNQLLGIA DRLEAGLEQV HLALKAQCST
EDVDSLVAQL TDELIAGCSQ PLGDIHETPS ATHLDQYLYQ LRTHHLSQIT EAALALKLGH
SELPAALEQA EDWLLRLRAL AEEPQNSLPD IVIWMLQGDK RVAYQRVPAH QVLFSRRGAN
YCGKNCGKLQ TIFLKYPMEK VPGARMPVQI RVKLWFGLSV DEKEFNQFAE GKLSVFAETY
ENETKLALVG NWGTTGLTYP KFSDVTGKIK LPKDSFRPSA GWTWAGDWFV CPEKTLLHDM
DAGHLSFVEE VFENQTRLPG GQWIYMSDNY TDVNGEKVLP KDDIECPLGW KWEDEEWSTD
LNRAVDEQGW EYSITIPPER KPKHWVPAEK MYYTHRRRRW VRLHRRDLSQ MEALKRHRQA
EAEGEGWEYA SLFGWKFHLE YRKTDAFRRR RWRRRMEPLE KTGPAAVFAL EGALGGVMDD
KSEDSMSVST LSFGVNRPTI SCIFDYGNRY HLRCYMYQAR DLAAMDKDSF SDPYAIVSFL
HQSQKTVVVK NTLNPTWDQT LIFYEIEIFG EPATVAEQPP SIVVELYDHD TYGADEFMGR
CICQPSLERM PRLAWFPLTR GSQPSGELLA SFELIQREKP AIHHIPGFEV QETSRILDES
EDTDLPYPPP QREANIYMVP QNIKPALQRT AIEILAWGLR NMKSYQLANI SSPSLVVECG
GQTVQSCVIR NLRKNPNFDI CTLFMEVMLP REELYCPPIT VKVIDNRQFG RRPVVGQCTI
RSLESFLCDP YSAESPSPQG GPDDVSLLSP GEDVLIDIDD KEPLIPIQLA DGLSSLAPTN
TASPPSSPHE EEFIDWWSKF FASIGEREKC GSYLEKDFDT LKVYDTQLEN VEAFEGLSDF
CNTFKLYRGK TQEETEDPSV IGEFKGLFKI YPLPEDPAIP MPPRQFHQLA AQGPQECLVR
IYIVRAFGLQ PKDPNGKCDP YIKISIGKKS VSDQDNYIPC TLEPVFGKMF ELTCTLPLEK
DLKITLYDYD LLSKDEKIGE TVVDLENRLL SKFGARCGLP QTYCVSGPNQ WRDQLRPSQL
LHLFCQQHRV KAPVYRTDRV MFQDKEYSIE EIEAGRIPNP HLGPVEERLA LHVLQQQGLV
PEHVESRPLY SPLQPDIEQG KLQMWVDLFP KALGRPGPPF NITPRRARRF FLRCIIWNTR
DVILDDLSLT GEKMSDIYVK GWMIGFEEHK QKTDVHYRSL GGEGNFNWRF IFPFDYLPAE
QVCTIAKKDA FWRLDKTESK IPARVVFQIW DNDKFSFDDF LGSLQLDLNR MPKPAKTAKK
CSLDQLDDAF HPEWFVSLFE QKTVKGWWPC VAEEGEKKIL AGKLEMTLEI VAESEHEERP
AGQGRDEPNM NPKLEDPRRP DTSFLWFTSP YKTMKFILWR RFRWAIILFI ILFILLLFLA
IFIYAFPNYA AMKLVKPFS*
speed 0.78 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