Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999692480674133 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970610)
  • known disease mutation: rs25127 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34647116A>CN/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.113A>C
cDNA.155A>C
g.8987A>C
AA changes Q38P Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 38
frameshift no
known variant Reference ID: rs111033646
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25127 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970610)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970610)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970610)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.2131
3.4551
(flanking)0.2730.997
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 increased8981wt: 0.2673 / mu: 0.3343 (marginal change - not scored)wt: TCAGCATATCCGCTACAACCCGCTGCAGGATGAGTGGGTGC
mu: TCAGCATATCCGCTACAACCCGCTGCCGGATGAGTGGGTGC		 accc|GCTG
Acc gained89930.48mu: CTACAACCCGCTGCCGGATGAGTGGGTGCTGGTGTCAGCTC atga|GTGG
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      38NDHQHIRYNPLQDEWVLVSAHRMK
mutated  not conserved    38NDHQHIRYNPLPDEWVLVSAHRM
Ptroglodytes  all identical  ENSPTRG00000020886  38NDHQHIRYNPLQDEWVLVSAHRM
Mmulatta  all identical  ENSMMUG00000020789  38SDHQHIRYNPLQDEWVLVSAHRM
Fcatus  all identical  ENSFCAG00000016304  38SEHQHIRYNPLQDEWVLVSAHRM
Mmusculus  all identical  ENSMUSG00000036073  19SEHQHIRYNPLQDEWVLVSAHRM
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000016445  23KEHQHLRYNPLRDTWVLVSAHRM
Drerio  all conserved  ENSDARG00000069543  23KEHQHLRYNPLRDSWVLVSAHRM
Dmelanogaster  not conserved  FBgn0263200  17SEHPHRRLNPLNGQWVLVCPHRT
Celegans  not conserved  ZK1058.3  14RYNPLIDEWVIVAVNRI
Xtropicalis  all conserved  ENSXETG00000013206  13EHQHIRYNPLRDDWLLVSAHRI
protein features
start (aa)end (aa)featuredetails 
7575METALZinc (Potential).might get lost (downstream of altered splice site)
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 113
cDNA position
(for ins/del: last normal base / first normal base)		 155
gDNA position
(for ins/del: last normal base / first normal base)		 8987
chromosomal position
(for ins/del: last normal base / first normal base)		 34647116
original gDNA sequence snippet TATCCGCTACAACCCGCTGCAGGATGAGTGGGTGCTGGTGT
altered gDNA sequence snippet TATCCGCTACAACCCGCTGCCGGATGAGTGGGTGCTGGTGT
original cDNA sequence snippet TATCCGCTACAACCCGCTGCAGGATGAGTGGGTGCTGGTGT
altered cDNA sequence snippet TATCCGCTACAACCCGCTGCCGGATGAGTGGGTGCTGGTGT
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 HIRYNPLPDE 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*
speed 0.84 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