Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999138413035      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs38277 (probable pathogenic)
  • known disease mutation at this position (HGMD CM074206)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648886G>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.815G>A
cDNA.857G>A
g.10757G>A
AA changes R272H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 272
frameshift no
known variant Reference ID: rs111033831
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC022

known as potential disease variant: rs38277 (probable pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074206)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074206)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074206)
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
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.1671
3.8951
(flanking)-0.270.966
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased10749wt: 0.9687 / mu: 0.9820 (marginal change - not scored)wt: ACCCCTGCTGAGCGT
mu: ACCCCTGCTGAGCAT		 CCCT|gctg
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      272VRRLPELTPAERDDLASIMKKLLT
mutated  not conserved    272VRRLPELTPAEHDDLASIMKKLL
Ptroglodytes  all identical  ENSPTRG00000020886  272VRRLPELTPAERDDLASIMKKLL
Mmulatta  all identical  ENSMMUG00000020789  272VQRLPELTPAERDDLASIMKKLL
Fcatus  all identical  ENSFCAG00000016304  272VRRLPELTPAERDDLACIMKKLL
Mmusculus  all identical  ENSMUSG00000036073  253VRRLPELNPAERDDLASIMKKLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  257RITELTAEERKGLADIMKRLL
Drerio  all identical  ENSDARG00000069543  257RLPDLTTQERDSLASIMKRLL
Dmelanogaster  all identical  FBgn0263200  251INDLTAEQRYNLALTIKELT
Celegans  all conserved  ZK1058.3  253LGEVEKQSLSEILRSLL
Xtropicalis  not conserved  ENSXETG00000013206  236LR-LQDLSQRRAPGLASIMKRLL
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 815
cDNA position
(for ins/del: last normal base / first normal base)		 857
gDNA position
(for ins/del: last normal base / first normal base)		 10757
chromosomal position
(for ins/del: last normal base / first normal base)		 34648886
original gDNA sequence snippet TGAGCTGACCCCTGCTGAGCGTGATGGTCAGTCTCCCAAGT
altered gDNA sequence snippet TGAGCTGACCCCTGCTGAGCATGATGGTCAGTCTCCCAAGT
original cDNA sequence snippet TGAGCTGACCCCTGCTGAGCGTGATGATCTAGCCTCCATCA
altered cDNA sequence snippet TGAGCTGACCCCTGCTGAGCATGATGATCTAGCCTCCATCA
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 EHDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.40 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