Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999980358 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990674)
  • known disease mutation: rs25310 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34649488C>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.986C>T
cDNA.1028C>T
g.11359C>T
AA changes S329F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 329
frameshift no
known variant Reference ID: rs111033803
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs25310 (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 CM990674)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990674)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990674)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6410.998
5.621
(flanking)-0.8260.789
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11357wt: 0.62 / mu: 0.80wt: TACTACCCTCCGCTCCTGCGCTCTGCCACTGTCCGGAAATT
mu: TACTACCCTCCGCTCCTGCGCTTTGCCACTGTCCGGAAATT		 gcgc|TCTG
Acc increased11367wt: 0.44 / mu: 0.68wt: CGCTCCTGCGCTCTGCCACTGTCCGGAAATTCATGGTTGGC
mu: CGCTCCTGCGCTTTGCCACTGTCCGGAAATTCATGGTTGGC		 actg|TCCG
Acc marginally increased11362wt: 0.8577 / mu: 0.8902 (marginal change - not scored)wt: CCCTCCGCTCCTGCGCTCTGCCACTGTCCGGAAATTCATGG
mu: CCCTCCGCTCCTGCGCTTTGCCACTGTCCGGAAATTCATGG		 ctgc|CACT
Acc marginally increased11370wt: 0.6531 / mu: 0.7457 (marginal change - not scored)wt: TCCTGCGCTCTGCCACTGTCCGGAAATTCATGGTTGGCTAC
mu: TCCTGCGCTTTGCCACTGTCCGGAAATTCATGGTTGGCTAC		 gtcc|GGAA
Acc marginally increased11364wt: 0.9639 / mu: 0.9753 (marginal change - not scored)wt: CTCCGCTCCTGCGCTCTGCCACTGTCCGGAAATTCATGGTT
mu: CTCCGCTCCTGCGCTTTGCCACTGTCCGGAAATTCATGGTT		 gcca|CTGT
Acc increased11349wt: 0.53 / mu: 0.62wt: ACGCTCATTACTACCCTCCGCTCCTGCGCTCTGCCACTGTC
mu: ACGCTCATTACTACCCTCCGCTCCTGCGCTTTGCCACTGTC		 ccgc|TCCT
distance from splice site 74
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      329LHAHYYPPLLRSATVRKFMVGYEM
mutated  not conserved    329LHAHYYPPLLRFATVRKFMVGYE
Ptroglodytes  all identical  ENSPTRG00000020886  329LHAHYYPPLLRSATVRKFMVGYE
Mmulatta  all identical  ENSMMUG00000020789  329LHAHYYPPLLRSATVRKFMVGYE
Fcatus  all identical  ENSFCAG00000016304  329LHAHYYPPLLRSATIRKFMVGYE
Mmusculus  all identical  ENSMUSG00000036073  310HYYPPLLRSATVRKFMVGYE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  314YPPLLRSATVKKFMVGYE
Drerio  all identical  ENSDARG00000069543  314YPPLLRSANIRKFMVGYE
Dmelanogaster  all identical  FBgn0263200  309YPPLLRSASVRKFMVGFE
Celegans  all identical  ZK1058.3  310LRSATVPKFLAGYE
Xtropicalis  all identical  ENSXETG00000013206  292LHAHFYPPLLRSATVRKFMVGYE
protein features no protein features affected
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 986
cDNA position
(for ins/del: last normal base / first normal base)		 1028
gDNA position
(for ins/del: last normal base / first normal base)		 11359
chromosomal position
(for ins/del: last normal base / first normal base)		 34649488
original gDNA sequence snippet CTACCCTCCGCTCCTGCGCTCTGCCACTGTCCGGAAATTCA
altered gDNA sequence snippet CTACCCTCCGCTCCTGCGCTTTGCCACTGTCCGGAAATTCA
original cDNA sequence snippet CTACCCTCCGCTCCTGCGCTCTGCCACTGTCCGGAAATTCA
altered cDNA sequence snippet CTACCCTCCGCTCCTGCGCTTTGCCACTGTCCGGAAATTCA
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 ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRFA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.90 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