Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.7759222488175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990652)
  • known disease mutation: rs25224 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648361G>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.595G>A
cDNA.637G>A
g.10232G>A
AA changes A199T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 199
frameshift no
known variant Reference ID: rs111033730
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs25224 (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 CM990652)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990652)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990652)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-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
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2710.914
0.9570.959
(flanking)1.250.973
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 increased10226wt: 0.6672 / mu: 0.7004 (marginal change - not scored)wt: GGGCCAGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAG
mu: GGGCCAGCAGTTTCCTGCCAGATATTACCCAGCGTGAGGAG		 ccag|ATAT
Donor increased10237wt: 0.22 / mu: 0.33wt: GCCCAGCGTGAGGAG
mu: ACCCAGCGTGAGGAG		 CCAG|cgtg
Donor increased10233wt: 0.61 / mu: 0.74wt: TATTGCCCAGCGTGA
mu: TATTACCCAGCGTGA		 TTGC|ccag
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      199QVWASSFLPDIAQREERSQQAYKS
mutated  not conserved    199QVWASSFLPDITQREERSQQAYK
Ptroglodytes  all identical  ENSPTRG00000020886  199QVWASSFLPDIAQREERSQQAYK
Mmulatta  all identical  ENSMMUG00000020789  199QVWASSFLPDIAQREERSQQTYK
Fcatus  all identical  ENSFCAG00000016304  199QVWASSFLPDIAQREERSQRAYQ
Mmusculus  all identical  ENSMUSG00000036073  180QVWASSFLPDIAQREERSQQTYH
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000016445  184QVWASDFLPNEPALS
Drerio  all identical  ENSDARG00000069543  184QVWASNFLPNEASLA
Dmelanogaster  not conserved  FBgn0263200  178QIWSCSFLPTEPQLKQ
Celegans  not conserved  ZK1058.3  180QLWASNYLPTLPMKKHESQ
Xtropicalis  not conserved  ENSXETG00000013206  162LVSIKANAPVLTP
protein features
start (aa)end (aa)featuredetails 
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 595
cDNA position
(for ins/del: last normal base / first normal base)		 637
gDNA position
(for ins/del: last normal base / first normal base)		 10232
chromosomal position
(for ins/del: last normal base / first normal base)		 34648361
original gDNA sequence snippet GCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCT
altered gDNA sequence snippet GCAGTTTCCTGCCAGATATTACCCAGCGTGAGGAGCGATCT
original cDNA sequence snippet GCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCT
altered cDNA sequence snippet GCAGTTTCCTGCCAGATATTACCCAGCGTGAGGAGCGATCT
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 FENKGAMMGC
SNPHPHCQVW ASSFLPDITQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
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