Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999781 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM994056)
  • known disease mutation: rs25214 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648160C>TN/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.556C>T
cDNA.598C>T
g.10031C>T
AA changes H186Y Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 186
frameshift no
known variant Reference ID: rs111033725
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs25214 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994056)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994056)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994056)
regulatory features H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
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)-0.130.982
5.211
(flanking)4.3131
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 increased10031wt: 0.4031 / mu: 0.4426 (marginal change - not scored)wt: GCTGTTCTAACCCCCACCCCCACTGCCAGGTAAGGGTGTCA
mu: GCTGTTCTAACCCCCACCCCTACTGCCAGGTAAGGGTGTCA		 cccc|ACTG
Acc marginally increased10027wt: 0.5619 / mu: 0.6215 (marginal change - not scored)wt: ATGGGCTGTTCTAACCCCCACCCCCACTGCCAGGTAAGGGT
mu: ATGGGCTGTTCTAACCCCCACCCCTACTGCCAGGTAAGGGT		 ccac|CCCC
Acc increased10039wt: 0.46 / mu: 0.58wt: AACCCCCACCCCCACTGCCAGGTAAGGGTGTCAGGGGCTCC
mu: AACCCCCACCCCTACTGCCAGGTAAGGGTGTCAGGGGCTCC		 ccag|GTAA
Acc marginally decreased10038wt: 0.8714 / mu: 0.8613 (marginal change - not scored)wt: TAACCCCCACCCCCACTGCCAGGTAAGGGTGTCAGGGGCTC
mu: TAACCCCCACCCCTACTGCCAGGTAAGGGTGTCAGGGGCTC		 gcca|GGTA
Acc increased10035wt: 0.53 / mu: 0.67wt: TTCTAACCCCCACCCCCACTGCCAGGTAAGGGTGTCAGGGG
mu: TTCTAACCCCCACCCCTACTGCCAGGTAAGGGTGTCAGGGG		 actg|CCAG
Donor marginally increased10034wt: 0.9629 / mu: 0.9737 (marginal change - not scored)wt: CCCACTGCCAGGTAA
mu: CCTACTGCCAGGTAA		 CACT|gcca
Acc gained100290.43mu: GGGCTGTTCTAACCCCCACCCCTACTGCCAGGTAAGGGTGT accc|CTAC
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      186GAMMGCSNPHPHCQVWASSFLPDI
mutated  all conserved    186SNPHPYCQVWASSFLPD
Ptroglodytes  all identical  ENSPTRG00000020886  186SNPHPHCQVWASSFLPD
Mmulatta  all identical  ENSMMUG00000020789  186SNPHPHCQVWASSFLPD
Fcatus  all identical  ENSFCAG00000016304  186SNPHPHCQVWASSFLPD
Mmusculus  all identical  ENSMUSG00000036073  167GAMMGCSNPHPHCQVWASSFLPD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  171GAMMGCSNPHPHCQVWASDFLPN
Drerio  all identical  ENSDARG00000069543  171GAMMGCSNPHPHCQVWASNFLPN
Dmelanogaster  all identical  FBgn0263200  165GAAMGCSNPHPHCQIWSCSFLPT
Celegans  all identical  ZK1058.3  167GAVVGCSNMHPHGQLWASNYLPT
Xtropicalis  not conserved  ENSXETG00000013206  153---CPCLCP------WVANAPAFTPG
protein features
start (aa)end (aa)featuredetails 
184184METALZinc (Potential).might get lost (downstream of altered splice site)
186186ACT_SITETele-UMP-histidine intermediate (By similarity).lost
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 556
cDNA position
(for ins/del: last normal base / first normal base)		 598
gDNA position
(for ins/del: last normal base / first normal base)		 10031
chromosomal position
(for ins/del: last normal base / first normal base)		 34648160
original gDNA sequence snippet GCTGTTCTAACCCCCACCCCCACTGCCAGGTAAGGGTGTCA
altered gDNA sequence snippet GCTGTTCTAACCCCCACCCCTACTGCCAGGTAAGGGTGTCA
original cDNA sequence snippet GCTGTTCTAACCCCCACCCCCACTGCCAGGTATGGGCCAGC
altered cDNA sequence snippet GCTGTTCTAACCCCCACCCCTACTGCCAGGTATGGGCCAGC
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
SNPHPYCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.34 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