Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.0182214111629497 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074201)
  • known disease mutation: rs25242 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648433C>AN/A show variant in all transcripts   IGV
HGNC symbol GALT
Ensembl transcript ID ENST00000450095
Genbank transcript ID NM_001258332
UniProt peptide P07902
alteration type single base exchange
alteration region CDS
DNA changes c.340C>A
cDNA.611C>A
g.10304C>A
AA changes R114S Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 114
frameshift no
known variant Reference ID: rs111033750
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs25242 (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 CM074201)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074201)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074201)
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)-0.0140.649
1.4030.642
(flanking)-0.2180.554
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased10306wt: 0.44 / mu: 0.57wt: AGCCGCCAGGAGCTA
mu: AGCAGCCAGGAGCTA		 CCGC|cagg
Donor increased10308wt: 0.44 / mu: 0.66wt: CCGCCAGGAGCTACT
mu: CAGCCAGGAGCTACT		 GCCA|ggag
Donor marginally increased10304wt: 0.9654 / mu: 0.9808 (marginal change - not scored)wt: ACAGCCGCCAGGAGC
mu: ACAGCAGCCAGGAGC		 AGCC|gcca
Donor marginally increased10296wt: 0.9515 / mu: 0.9717 (marginal change - not scored)wt: AATGGAGTACAGCCG
mu: AATGGAGTACAGCAG		 TGGA|gtac
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      114QHGEPLLMEYSRQELLRKERLVLT
mutated  not conserved    114QHGEPLLMEYSSQELLRK
Ptroglodytes  all identical  ENSPTRG00000020886  223QHGEPLLMEYSRQELLRKERLVL
Mmulatta  all identical  ENSMMUG00000020789  223QHGEPLLMEYSRQELLRKERLVL
Fcatus  not conserved  ENSFCAG00000016304  223QHGEPLLMEYGHQELLRRERLVL
Mmusculus  not conserved  ENSMUSG00000036073  204QHGKPLLLEYGHQELLRKERLVL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  208KHGEPLLLQYAREEAAKEERLVL
Drerio  all identical  ENSDARG00000069543  208KHGEPMLVQYARMEAQAQERVVV
Dmelanogaster  not conserved  FBgn0263200  202TNERPMLADYVERELQRQERIVI
Celegans  not conserved  ZK1058.3  204KHGKVMLMDYLEQETLKKERIIM
Xtropicalis  no alignment  ENSXETG00000013206  n/a
protein features
start (aa)end (aa)featuredetails 
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 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 1084 / 1084
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 272 / 272
chromosome 9
strand 1
last intron/exon boundary 1004
theoretical NMD boundary in CDS 682
length of CDS 813
coding sequence (CDS) position 340
cDNA position
(for ins/del: last normal base / first normal base)		 611
gDNA position
(for ins/del: last normal base / first normal base)		 10304
chromosomal position
(for ins/del: last normal base / first normal base)		 34648433
original gDNA sequence snippet CCCTGCTAATGGAGTACAGCCGCCAGGAGCTACTCAGGAAG
altered gDNA sequence snippet CCCTGCTAATGGAGTACAGCAGCCAGGAGCTACTCAGGAAG
original cDNA sequence snippet CCCTGCTAATGGAGTACAGCCGCCAGGAGCTACTCAGGAAG
altered cDNA sequence snippet CCCTGCTAATGGAGTACAGCAGCCAGGAGCTACTCAGGAAG
wildtype AA sequence MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
mutated AA sequence MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSSQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *
speed 1.37 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