Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.0705079333913336 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990651)
  • known disease mutation: rs25223 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648360T>GN/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.594T>G
cDNA.636T>G
g.10231T>G
AA changes I198M Score: 10 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs111033729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs25223 (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 CM990651)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990651)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990651)
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)0.8290.923
-0.2710.914
(flanking)0.9570.959
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased10230wt: 0.22 / mu: 0.74wt: CAGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAGCGAT
mu: CAGCAGTTTCCTGCCAGATATGGCCCAGCGTGAGGAGCGAT		 atat|TGCC
Acc increased10225wt: 0.60 / mu: 0.67wt: TGGGCCAGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGA
mu: TGGGCCAGCAGTTTCCTGCCAGATATGGCCCAGCGTGAGGA		 gcca|GATA
Acc marginally increased10226wt: 0.6672 / mu: 0.6914 (marginal change - not scored)wt: GGGCCAGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAG
mu: GGGCCAGCAGTTTCCTGCCAGATATGGCCCAGCGTGAGGAG		 ccag|ATAT
Donor increased10225wt: 0.81 / mu: 1.00wt: CTGCCAGATATTGCC
mu: CTGCCAGATATGGCC		 GCCA|gata
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198CQVWASSFLPDIAQREERSQQAYK
mutated  all conserved    198CQVWASSFLPDMAQREERSQQAY
Ptroglodytes  all identical  ENSPTRG00000020886  198CQVWASSFLPDIAQREERSQQAY
Mmulatta  all identical  ENSMMUG00000020789  198CQVWASSFLPDIAQREERSQQTY
Fcatus  all identical  ENSFCAG00000016304  198CQVWASSFLPDIAQREERSQRAY
Mmusculus  all identical  ENSMUSG00000036073  179CQVWASSFLPDIAQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000016445  183CQVWASDFLPNEPALS
Drerio  not conserved  ENSDARG00000069543  183CQVWASNFLPNEASLA
Dmelanogaster  not conserved  FBgn0263200  177CQIWSCSFLPTEPQLKQ
Celegans  all conserved  ZK1058.3  179GQLWASNYLPTLPMKKHESQ
Xtropicalis  all conserved  ENSXETG00000013206  161LVSIKANAPVLT
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 594
cDNA position
(for ins/del: last normal base / first normal base)		 636
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 34648360
original gDNA sequence snippet AGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAGCGATC
altered gDNA sequence snippet AGCAGTTTCCTGCCAGATATGGCCCAGCGTGAGGAGCGATC
original cDNA sequence snippet AGCAGTTTCCTGCCAGATATTGCCCAGCGTGAGGAGCGATC
altered cDNA sequence snippet AGCAGTTTCCTGCCAGATATGGCCCAGCGTGAGGAGCGATC
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 ASSFLPDMAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 1.33 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