Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999979914 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993300)
  • known disease mutation: rs1102 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:100382048G>CN/A show variant in all transcripts   IGV
HGNC symbol AGL
Ensembl transcript ID ENST00000370165
Genbank transcript ID NM_000644
UniProt peptide P35573
alteration type single base exchange
alteration region CDS
DNA changes c.4342G>C
cDNA.4480G>C
g.66409G>C
AA changes G1448R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1448
frameshift no
known variant Reference ID: rs118203964
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1102 (pathogenic for Glycogen storage disease IIIa) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993300)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993300)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993300)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3791
5.861
(flanking)5.861
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased66404wt: 0.80 / mu: 0.97wt: TTATCACCAAGGACC
mu: TTATCACCAACGACC		 ATCA|ccaa
Donor increased66407wt: 0.38 / mu: 0.47wt: TCACCAAGGACCTGT
mu: TCACCAACGACCTGT		 ACCA|agga
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1448YNLAKGFNYHQGPEWLWPIGYFLR
mutated  not conserved    1448KGFNYHQRPEWLWPIGYFL
Ptroglodytes  all identical  ENSPTRG00000000997  1448KGFNYHQGPEWLWPIGYFL
Mmulatta  all identical  ENSMMUG00000021441  1449AKGFNYHQGPEWLWPIGYFL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000033400  1448RGFNYHQGPEWLWPIGYFL
Ggallus  all identical  ENSGALG00000005407  1447RGFNYHQGPEWLWPIGYFL
Trubripes  all identical  ENSTRUG00000012741  1448RGFNYHQGPEWLWPVGYFL
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0034618  1539CTVAHGANYHQGPEWVWPIGFYL
Celegans  all identical  R06A4.8  1378KKTAKGWNYHQGPEWLFVAGYYL
Xtropicalis  all identical  ENSXETG00000013185  1448SKGFNYHQGPEWMWPIGYFL
protein features
start (aa)end (aa)featuredetails 
15321532REGIONAmylo-1,6-glucosidase. - EXACT POSITION UNKNOWNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4599 / 4599
position (AA) of stopcodon in wt / mu AA sequence 1533 / 1533
position of stopcodon in wt / mu cDNA 4737 / 4737
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 139 / 139
chromosome 1
strand 1
last intron/exon boundary 4620
theoretical NMD boundary in CDS 4431
length of CDS 4599
coding sequence (CDS) position 4342
cDNA position
(for ins/del: last normal base / first normal base)		 4480
gDNA position
(for ins/del: last normal base / first normal base)		 66409
chromosomal position
(for ins/del: last normal base / first normal base)		 100382048
original gDNA sequence snippet AAGGTTTCAATTATCACCAAGGACCTGTAAGAATTTCATTT
altered gDNA sequence snippet AAGGTTTCAATTATCACCAACGACCTGTAAGAATTTCATTT
original cDNA sequence snippet AAGGTTTCAATTATCACCAAGGACCTGAGTGGCTGTGGCCT
altered cDNA sequence snippet AAGGTTTCAATTATCACCAACGACCTGAGTGGCTGTGGCCT
wildtype AA sequence MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE
KFRSLDWENP TEREDDSDKY CKLNLQQSGS FQYYFLQGNE KSGGGYIVVD PILRVGADNH
VLPLDCVTLQ TFLAKCLGPF DEWESRLRVA KESGYNMIHF TPLQTLGLSR SCYSLANQLE
LNPDFSRPNR KYTWNDVGQL VEKLKKEWNV ICITDVVYNH TAANSKWIQE HPECAYNLVN
SPHLKPAWVL DRALWRFSCD VAEGKYKEKG IPALIENDHH MNSIRKIIWE DIFPKLKLWE
FFQVDVNKAV EQFRRLLTQE NRRVTKSDPN QHLTIIQDPE YRRFGCTVDM NIALTTFIPH
DKGPAAIEEC CNWFHKRMEE LNSEKHRLIN YHQEQAVNCL LGNVFYERLA GHGPKLGPVT
RKHPLVTRYF TFPFEEIDFS MEESMIHLPN KACFLMAHNG WVMGDDPLRN FAEPGSEVYL
RRELICWGDS VKLRYGNKPE DCPYLWAHMK KYTEITATYF QGVRLDNCHS TPLHVAEYML
DAARNLQPNL YVVAELFTGS EDLDNVFVTR LGISSLIREA MSAYNSHEEG RLVYRYGGEP
VGSFVQPCLR PLMPAIAHAL FMDITHDNEC PIVHRSAYDA LPSTTIVSMA CCASGSTRGY
DELVPHQISV VSEERFYTKW NPEALPSNTG EVNFQSGIIA ARCAISKLHQ ELGAKGFIQV
YVDQVDEDIV AVTRHSPSIH QSVVAVSRTA FRNPKTSFYS KEVPQMCIPG KIEEVVLEAR
TIERNTKPYR KDENSINGTP DITVEIREHI QLNESKIVKQ AGVATKGPNE YIQEIEFENL
SPGSVIIFRV SLDPHAQVAV GILRNHLTQF SPHFKSGSLA VDNADPILKI PFASLASRLT
LAELNQILYR CESEEKEDGG GCYDIPNWSA LKYAGLQGLM SVLAEIRPKN DLGHPFCNNL
RSGDWMIDYV SNRLISRSGT IAEVGKWLQA MFFYLKQIPR YLIPCYFDAI LIGAYTTLLD
TAWKQMSSFV QNGSTFVKHL SLGSVQLCGV GKFPSLPILS PALMDVPYRL NEITKEKEQC
CVSLAAGLPH FSSGIFRCWG RDTFIALRGI LLITGRYVEA RNIILAFAGT LRHGLIPNLL
GEGIYARYNC RDAVWWWLQC IQDYCKMVPN GLDILKCPVS RMYPTDDSAP LPAGTLDQPL
FEVIQEAMQK HMQGIQFRER NAGPQIDRNM KDEGFNITAG VDEETGFVYG GNRFNCGTWM
DKMGESDRAR NRGIPATPRD GSAVEIVGLS KSAVRWLLEL SKKNIFPYHE VTVKRHGKAI
KVSYDEWNRK IQDNFEKLFH VSEDPSDLNE KHPNLVHKRG IYKDSYGASS PWCDYQLRPN
FTIAMVVAPE LFTTEKAWKA LEIAEKKLLG PLGMKTLDPD DMVYCGIYDN ALDNDNYNLA
KGFNYHQGPE WLWPIGYFLR AKLYFSRLMG PETTAKTIVL VKNVLSRHYV HLERSPWKGL
PELTNENAQY CPFSCETQAW SIATILETLY DL*
mutated AA sequence MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE
KFRSLDWENP TEREDDSDKY CKLNLQQSGS FQYYFLQGNE KSGGGYIVVD PILRVGADNH
VLPLDCVTLQ TFLAKCLGPF DEWESRLRVA KESGYNMIHF TPLQTLGLSR SCYSLANQLE
LNPDFSRPNR KYTWNDVGQL VEKLKKEWNV ICITDVVYNH TAANSKWIQE HPECAYNLVN
SPHLKPAWVL DRALWRFSCD VAEGKYKEKG IPALIENDHH MNSIRKIIWE DIFPKLKLWE
FFQVDVNKAV EQFRRLLTQE NRRVTKSDPN QHLTIIQDPE YRRFGCTVDM NIALTTFIPH
DKGPAAIEEC CNWFHKRMEE LNSEKHRLIN YHQEQAVNCL LGNVFYERLA GHGPKLGPVT
RKHPLVTRYF TFPFEEIDFS MEESMIHLPN KACFLMAHNG WVMGDDPLRN FAEPGSEVYL
RRELICWGDS VKLRYGNKPE DCPYLWAHMK KYTEITATYF QGVRLDNCHS TPLHVAEYML
DAARNLQPNL YVVAELFTGS EDLDNVFVTR LGISSLIREA MSAYNSHEEG RLVYRYGGEP
VGSFVQPCLR PLMPAIAHAL FMDITHDNEC PIVHRSAYDA LPSTTIVSMA CCASGSTRGY
DELVPHQISV VSEERFYTKW NPEALPSNTG EVNFQSGIIA ARCAISKLHQ ELGAKGFIQV
YVDQVDEDIV AVTRHSPSIH QSVVAVSRTA FRNPKTSFYS KEVPQMCIPG KIEEVVLEAR
TIERNTKPYR KDENSINGTP DITVEIREHI QLNESKIVKQ AGVATKGPNE YIQEIEFENL
SPGSVIIFRV SLDPHAQVAV GILRNHLTQF SPHFKSGSLA VDNADPILKI PFASLASRLT
LAELNQILYR CESEEKEDGG GCYDIPNWSA LKYAGLQGLM SVLAEIRPKN DLGHPFCNNL
RSGDWMIDYV SNRLISRSGT IAEVGKWLQA MFFYLKQIPR YLIPCYFDAI LIGAYTTLLD
TAWKQMSSFV QNGSTFVKHL SLGSVQLCGV GKFPSLPILS PALMDVPYRL NEITKEKEQC
CVSLAAGLPH FSSGIFRCWG RDTFIALRGI LLITGRYVEA RNIILAFAGT LRHGLIPNLL
GEGIYARYNC RDAVWWWLQC IQDYCKMVPN GLDILKCPVS RMYPTDDSAP LPAGTLDQPL
FEVIQEAMQK HMQGIQFRER NAGPQIDRNM KDEGFNITAG VDEETGFVYG GNRFNCGTWM
DKMGESDRAR NRGIPATPRD GSAVEIVGLS KSAVRWLLEL SKKNIFPYHE VTVKRHGKAI
KVSYDEWNRK IQDNFEKLFH VSEDPSDLNE KHPNLVHKRG IYKDSYGASS PWCDYQLRPN
FTIAMVVAPE LFTTEKAWKA LEIAEKKLLG PLGMKTLDPD DMVYCGIYDN ALDNDNYNLA
KGFNYHQRPE WLWPIGYFLR AKLYFSRLMG PETTAKTIVL VKNVLSRHYV HLERSPWKGL
PELTNENAQY CPFSCETQAW SIATILETLY DL*
speed 1.04 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