Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999989573555 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM095713)
  • known disease mutation at this position (HGMD CM920294)
  • known disease mutation: rs3616 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34648116T>CN/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.512T>C
cDNA.554T>C
g.9987T>C
AA changes F171S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 171
frameshift no
known variant Reference ID: rs111033715
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs3616 (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 CM920294)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM095713)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM095713)
known disease mutation at this position, please check HGMD for details (HGMD ID CM095713)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM095713)
known disease mutation at this position, please check HGMD for details (HGMD ID CM095713)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920294)
regulatory features 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)4.3131
4.3131
(flanking)1.8641
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased9981wt: 0.24 / mu: 0.32wt: GCTCCGTATCCCTATCTGATAGATCTTTGAAAACAAAGGTG
mu: GCTCCGTATCCCTATCTGATAGATCTCTGAAAACAAAGGTG		 gata|GATC
Donor marginally increased9988wt: 0.8336 / mu: 0.8616 (marginal change - not scored)wt: ATCTTTGAAAACAAA
mu: ATCTCTGAAAACAAA		 CTTT|gaaa
Donor marginally increased9992wt: 0.9317 / mu: 0.9643 (marginal change - not scored)wt: TTGAAAACAAAGGTG
mu: CTGAAAACAAAGGTG		 GAAA|acaa
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      171ELGAQYPWVQIFENKGAMMGCSNP
mutated  not conserved    171ELGAQYPWVQISENKGAMMGC
Ptroglodytes  all identical  ENSPTRG00000020886  171ELGAQYPWVQIFENKGAMMGC
Mmulatta  all identical  ENSMMUG00000020789  171ELGAQYPWVQIFENKGAMMGC
Fcatus  all identical  ENSFCAG00000016304  171ELGAQYPWVQIFENKGAMMGC
Mmusculus  all identical  ENSMUSG00000036073  152ELGAQYPWVQIFENKGAMMGCSN
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016445  156ELGSTYRWVQIFENKGAMMGCSN
Drerio  all identical  ENSDARG00000069543  156ELGATYAWVQIFENKGAMMGCSN
Dmelanogaster  all identical  FBgn0263200  150ELSAKYAWVQIFENKGAAMGCSN
Celegans  all identical  ZK1058.3  152ELGPKYEWVQIFENRGAVVGCSN
Xtropicalis  all conserved  ENSXETG00000013206  138PLGCKCPCLYPWVGYYKSK---CPCLC
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 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 512
cDNA position
(for ins/del: last normal base / first normal base)		 554
gDNA position
(for ins/del: last normal base / first normal base)		 9987
chromosomal position
(for ins/del: last normal base / first normal base)		 34648116
original gDNA sequence snippet TATCCCTATCTGATAGATCTTTGAAAACAAAGGTGCCATGA
altered gDNA sequence snippet TATCCCTATCTGATAGATCTCTGAAAACAAAGGTGCCATGA
original cDNA sequence snippet GTACCCTTGGGTGCAGATCTTTGAAAACAAAGGTGCCATGA
altered cDNA sequence snippet GTACCCTTGGGTGCAGATCTCTGAAAACAAAGGTGCCATGA
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 SENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*
speed 0.97 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