Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999078187797 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980578)
  • known disease mutation: rs6668 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:71909727C>TN/A show variant in all transcripts   IGV
HGNC symbol DYSF
Ensembl transcript ID ENST00000409651
Genbank transcript ID NM_001130982
UniProt peptide O75923
alteration type single base exchange
alteration region CDS
DNA changes c.6220C>T
cDNA.6361C>T
g.228876C>T
AA changes R2074C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 2074
frameshift no
known variant Reference ID: rs121908955
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs6668 (pathogenic for Autosomal recessive limb-girdle muscular dystrophy type 2B|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 CM980578)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980578)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980578)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.651
1.0791
(flanking)5.4291
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased228883wt: 0.2192 / mu: 0.2321 (marginal change - not scored)wt: CATCCTGTGGCGGCGTTTCCGGTGGGCCATCATCCTCTTCA
mu: CATCCTGTGGCGGTGTTTCCGGTGGGCCATCATCCTCTTCA		 tccg|GTGG
distance from splice site 68
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      2074PYKTMKFILWRRFRWAIILFIILF
mutated  not conserved    2074PYKTMKFILWRCFRWAIILFIIL
Ptroglodytes  all identical  ENSPTRG00000012049  2035PYKTMKFILWRRFRWAIILFIIL
Mmulatta  all identical  ENSMMUG00000007176  2012MKFILWRRFRWAIILFIIL
Fcatus  all identical  ENSFCAG00000004357  2012ILWRRFRCAIILFIIL
Mmusculus  all identical  ENSMUSG00000033788  2062PYKTMKFILWRRFRCAIILFIIL
Ggallus  all identical  ENSGALG00000016105  870PYKTLKYILWRRYKWLLILAIVL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000007370  1802PYKTFRFIVWRRFKWLILGLFIL
Dmelanogaster  no homologue    
Celegans  no alignment  T05E8.1  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
20682080TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6339 / 6339
position (AA) of stopcodon in wt / mu AA sequence 2113 / 2113
position of stopcodon in wt / mu cDNA 6480 / 6480
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 6442
theoretical NMD boundary in CDS 6250
length of CDS 6339
coding sequence (CDS) position 6220
cDNA position
(for ins/del: last normal base / first normal base)		 6361
gDNA position
(for ins/del: last normal base / first normal base)		 228876
chromosomal position
(for ins/del: last normal base / first normal base)		 71909727
original gDNA sequence snippet TGAAGTTCATCCTGTGGCGGCGTTTCCGGTGGGCCATCATC
altered gDNA sequence snippet TGAAGTTCATCCTGTGGCGGTGTTTCCGGTGGGCCATCATC
original cDNA sequence snippet TGAAGTTCATCCTGTGGCGGCGTTTCCGGTGGGCCATCATC
altered cDNA sequence snippet TGAAGTTCATCCTGTGGCGGTGTTTCCGGTGGGCCATCATC
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 GGEIEEEPAG AVKPSKASDL
DDYLGFLPTF GPCYINLYGS PREFTGFPDP YTELNTGKGE GVAYRGRLLL SLETKLVEHS
EQKVEDLPAD DILRVEKYLR RRKYSLFAAF YSATMLQDVD DAIQFEVSIG NYGNKFDMTC
LPLASTTQYS RAVFDGCHYY YLPWGNVKPV VVLSSYWEDI SHRIETQNQL LGIADRLEAG
LEQVHLALKA QCSTEDVDSL VAQLTDELIA GCSQPLGDIH ETPSATHLDQ YLYQLRTHHL
SQITEAALAL KLGHSELPAA LEQAEDWLLR LRALAEEPQN SLPDIVIWML QGDKRVAYQR
VPAHQVLFSR RGANYCGKNC GKLQTIFLKY PMEKVPGARM PVQIRVKLWF GLSVDEKEFN
QFAEGKLSVF AETYENETKL ALVGNWGTTG LTYPKFSDVT GKIKLPKDSF RPSAGWTWAG
DWFVCPEKTL LHDMDAGHLS FVEEVFENQT RLPGGQWIYM SDNYTDVNGE KVLPKDDIEC
PLGWKWEDEE WSTDLNRAVD EQGWEYSITI PPERKPKHWV PAEKMYYTHR RRRWVRLRRR
DLSQMEALKR HRQAEAEGEG WEYASLFGWK FHLEYRKTDA FRRRRWRRRM EPLEKTGPAA
VFALEGALGG VMDDKSEDSM SVSTLSFGVN RPTISCIFDY GNRYHLRCYM YQARDLAAMD
KDSFSDPYAI VSFLHQSQKT VVVKNTLNPT WDQTLIFYEI EIFGEPATVA EQPPSIVVEL
YDHDTYGADE FMGRCICQPS LERMPRLAWF PLTRGSQPSG ELLASFELIQ REKPAIHHIP
GFEVQETSRI LDESEDTDLP YPPPQREANI YMVPQNIKPA LQRTAIEILA WGLRNMKSYQ
LANISSPSLV VECGGQTVQS CVIRNLRKNP NFDICTLFME VMLPREELYC PPITVKVIDN
RQFGRRPVVG QCTIRSLESF LCDPYSAESP SPQGGPDDVS LLSPGEDVLI DIDDKEPLIP
IQEEEFIDWW SKFFASIGER EKCGSYLEKD FDTLKVYDTQ LENVEAFEGL SDFCNTFKLY
RGKTQEETED PSVIGEFKGL FKIYPLPEDP AIPMPPRQFH QLAAQGPQEC LVRIYIVRAF
GLQPKDPNGK CDPYIKISIG KKSVSDQDNY IPCTLEPVFG KMFELTCTLP LEKDLKITLY
DYDLLSKDEK IGETVVDLEN RLLSKFGARC GLPQTYCVSG PNQWRDQLRP SQLLHLFCQQ
HRVKAPVYRT DRVMFQDKEY SIEEIEAGRI PNPHLGPVEE RLALHVLQQQ GLVPEHVESR
PLYSPLQPDI EQGKLQMWVD LFPKALGRPG PPFNITPRRA RRFFLRCIIW NTRDVILDDL
SLTGEKMSDI YVKGWMIGFE EHKQKTDVHY RSLGGEGNFN WRFIFPFDYL PAEQVCTIAK
KDAFWRLDKT ESKIPARVVF QIWDNDKFSF DDFLGSLQLD LNRMPKPAKT AKKCSLDQLD
DAFHPEWFVS LFEQKTVKGW WPCVAEEGEK KILAGKLEMT LEIVAESEHE ERPAGQGRDE
PNMNPKLEDP RRPDTSFLWF TSPYKTMKFI LWRRFRWAII LFIILFILLL FLAIFIYAFP
NYAAMKLVKP FS*
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 GGEIEEEPAG AVKPSKASDL
DDYLGFLPTF GPCYINLYGS PREFTGFPDP YTELNTGKGE GVAYRGRLLL SLETKLVEHS
EQKVEDLPAD DILRVEKYLR RRKYSLFAAF YSATMLQDVD DAIQFEVSIG NYGNKFDMTC
LPLASTTQYS RAVFDGCHYY YLPWGNVKPV VVLSSYWEDI SHRIETQNQL LGIADRLEAG
LEQVHLALKA QCSTEDVDSL VAQLTDELIA GCSQPLGDIH ETPSATHLDQ YLYQLRTHHL
SQITEAALAL KLGHSELPAA LEQAEDWLLR LRALAEEPQN SLPDIVIWML QGDKRVAYQR
VPAHQVLFSR RGANYCGKNC GKLQTIFLKY PMEKVPGARM PVQIRVKLWF GLSVDEKEFN
QFAEGKLSVF AETYENETKL ALVGNWGTTG LTYPKFSDVT GKIKLPKDSF RPSAGWTWAG
DWFVCPEKTL LHDMDAGHLS FVEEVFENQT RLPGGQWIYM SDNYTDVNGE KVLPKDDIEC
PLGWKWEDEE WSTDLNRAVD EQGWEYSITI PPERKPKHWV PAEKMYYTHR RRRWVRLRRR
DLSQMEALKR HRQAEAEGEG WEYASLFGWK FHLEYRKTDA FRRRRWRRRM EPLEKTGPAA
VFALEGALGG VMDDKSEDSM SVSTLSFGVN RPTISCIFDY GNRYHLRCYM YQARDLAAMD
KDSFSDPYAI VSFLHQSQKT VVVKNTLNPT WDQTLIFYEI EIFGEPATVA EQPPSIVVEL
YDHDTYGADE FMGRCICQPS LERMPRLAWF PLTRGSQPSG ELLASFELIQ REKPAIHHIP
GFEVQETSRI LDESEDTDLP YPPPQREANI YMVPQNIKPA LQRTAIEILA WGLRNMKSYQ
LANISSPSLV VECGGQTVQS CVIRNLRKNP NFDICTLFME VMLPREELYC PPITVKVIDN
RQFGRRPVVG QCTIRSLESF LCDPYSAESP SPQGGPDDVS LLSPGEDVLI DIDDKEPLIP
IQEEEFIDWW SKFFASIGER EKCGSYLEKD FDTLKVYDTQ LENVEAFEGL SDFCNTFKLY
RGKTQEETED PSVIGEFKGL FKIYPLPEDP AIPMPPRQFH QLAAQGPQEC LVRIYIVRAF
GLQPKDPNGK CDPYIKISIG KKSVSDQDNY IPCTLEPVFG KMFELTCTLP LEKDLKITLY
DYDLLSKDEK IGETVVDLEN RLLSKFGARC GLPQTYCVSG PNQWRDQLRP SQLLHLFCQQ
HRVKAPVYRT DRVMFQDKEY SIEEIEAGRI PNPHLGPVEE RLALHVLQQQ GLVPEHVESR
PLYSPLQPDI EQGKLQMWVD LFPKALGRPG PPFNITPRRA RRFFLRCIIW NTRDVILDDL
SLTGEKMSDI YVKGWMIGFE EHKQKTDVHY RSLGGEGNFN WRFIFPFDYL PAEQVCTIAK
KDAFWRLDKT ESKIPARVVF QIWDNDKFSF DDFLGSLQLD LNRMPKPAKT AKKCSLDQLD
DAFHPEWFVS LFEQKTVKGW WPCVAEEGEK KILAGKLEMT LEIVAESEHE ERPAGQGRDE
PNMNPKLEDP RRPDTSFLWF TSPYKTMKFI LWRCFRWAII LFIILFILLL FLAIFIYAFP
NYAAMKLVKP FS*
speed 1.14 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