Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999653343 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065207)
  • known disease mutation: rs25203 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648128G>AN/A show variant in all transcripts   IGV
HGNC symbol GALT
Ensembl transcript ID ENST00000378842
Genbank transcript ID NM_000155
UniProt peptide P07902
alteration type single base exchange
alteration region CDS
DNA changes c.524G>A
cDNA.566G>A
g.9999G>A
AA changes G175D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 175
frameshift no
known variant Reference ID: rs111033718
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs25203 (pathogenic for Galactosemia|Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not specified) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065207)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065207)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.211
5.211
(flanking)-0.0510.994
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased10000wt: 0.83 / mu: 0.92wt: AAAGGTGCCATGATG
mu: AAAGATGCCATGATG		 AGGT|gcca
Donor increased9995wt: 0.38 / mu: 0.95wt: AAAACAAAGGTGCCA
mu: AAAACAAAGATGCCA		 AACA|aagg
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      175QYPWVQIFENKGAMMGCSNPHPHC
mutated  not conserved    175QYPWVQIFENKDAMMGC
Ptroglodytes  all identical  ENSPTRG00000020886  175QYPWVQIFENKGAMMGC
Mmulatta  all identical  ENSMMUG00000020789  175QYPWVQIFENKGAMMGC
Fcatus  all identical  ENSFCAG00000016304  175QYPWVQIFENKGAMMGC
Mmusculus  all identical  ENSMUSG00000036073  156QYPWVQIFENKGAMMGCSNPHPH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  160TYRWVQIFENKGAMMGCSNPHPH
Drerio  all identical  ENSDARG00000069543  160TYAWVQIFENKGAMMGCSNPHPH
Dmelanogaster  all identical  FBgn0263200  154KYAWVQIFENKGAAMGCSNPHPH
Celegans  all identical  ZK1058.3  156KYEWVQIFENRGAVVGCSNMHPH
Xtropicalis  not conserved  ENSXETG00000013206  142KCPCLYPWVGYYKSK---CPCLCP---
protein features
start (aa)end (aa)featuredetails 
184184METALZinc (Potential).might get lost (downstream of altered splice site)
186186ACT_SITETele-UMP-histidine intermediate (By similarity).might get lost (downstream of altered splice site)
202202METALIron (Potential).might get lost (downstream of altered splice site)
258259CONFLICTRR -> VG (in Ref. 1; AAC83409).might get lost (downstream of altered splice site)
301301METALIron (Potential).might get lost (downstream of altered splice site)
319319METALIron (Potential).might get lost (downstream of altered splice site)
321321METALIron (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1140 / 1140
position (AA) of stopcodon in wt / mu AA sequence 380 / 380
position of stopcodon in wt / mu cDNA 1182 / 1182
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 43 / 43
chromosome 9
strand 1
last intron/exon boundary 1102
theoretical NMD boundary in CDS 1009
length of CDS 1140
coding sequence (CDS) position 524
cDNA position
(for ins/del: last normal base / first normal base)		 566
gDNA position
(for ins/del: last normal base / first normal base)		 9999
chromosomal position
(for ins/del: last normal base / first normal base)		 34648128
original gDNA sequence snippet ATAGATCTTTGAAAACAAAGGTGCCATGATGGGCTGTTCTA
altered gDNA sequence snippet ATAGATCTTTGAAAACAAAGATGCCATGATGGGCTGTTCTA
original cDNA sequence snippet GCAGATCTTTGAAAACAAAGGTGCCATGATGGGCTGTTCTA
altered cDNA sequence snippet GCAGATCTTTGAAAACAAAGATGCCATGATGGGCTGTTCTA
wildtype AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
mutated AA sequence MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKDAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.69 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