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 ENST00000409651
Genbank transcript ID NM_001130982
UniProt peptide O75923
alteration type single base exchange
alteration region CDS
DNA changes c.3233G>A
cDNA.3374G>A
g.116983G>A
AA changes R1078H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1078
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      1078YTHRRRRWVRLRRRDLSQMEALKR
mutated  not conserved    1078YTHRRRRWVRLHRR
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  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 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 3233
cDNA position
(for ins/del: last normal base / first normal base)		 3374
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 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 RRRWVRLHRR
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*
speed 1.06 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