Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000350028
Querying Taster for transcript #2: ENST00000396202
MT speed 0 s - this script 3.17268 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SAMM50polymorphism_automatic0.999999993464369simple_aaeaffectedD110Gsingle base exchangers3761472show file
SAMM50polymorphism_automatic1without_aaeaffectedsingle base exchangers3761472show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 6.53563118763359e-09 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:44368122A>GN/A show variant in all transcripts   IGV
HGNC symbol SAMM50
Ensembl transcript ID ENST00000350028
Genbank transcript ID NM_015380
UniProt peptide Q9Y512
alteration type single base exchange
alteration region CDS
DNA changes c.329A>G
cDNA.486A>G
g.16822A>G
AA changes D110G Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 110
frameshift no
known variant Reference ID: rs3761472
databasehomozygous (G/G)heterozygousallele carriers
1000G1778691046
ExAC29881912322111
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9911
3.1371
(flanking)-0.3160.953
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased16816wt: 0.49 / mu: 0.55wt: TTTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAATG
mu: TTTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATG		 tagg|TGAT
Acc marginally increased16814wt: 0.9852 / mu: 0.9861 (marginal change - not scored)wt: TGTTTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAA
mu: TGTTTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAA		 ttta|GGTG
Acc marginally increased16819wt: 0.6583 / mu: 0.6617 (marginal change - not scored)wt: AATATTTTTTTATTTAGGTGATGACGCACTTCCAAATGGGT
mu: AATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGGGT		 gtga|TGAC
Acc marginally increased16817wt: 0.2437 / mu: 0.2547 (marginal change - not scored)wt: TTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAATGG
mu: TTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGG		 aggt|GATG
Donor marginally decreased16815wt: 0.9918 / mu: 0.9915 (marginal change - not scored)wt: ATTTAGGTGATGACG
mu: ATTTAGGTGATGGCG		 TTAG|gtga
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      110VDVLIDTCQGDDALPNGLDVTFEV
mutated  not conserved    110VDVLIDTCQGDGALPNGLDVTF
Ptroglodytes  all identical  ENSPTRG00000014483  110VDVLIDTCQGDDALPNGLDVTF
Mmulatta  all identical  ENSMMUG00000015446  110VDVLIDTCQGDDALPNGLDVTF
Fcatus  all identical  ENSFCAG00000007342  103VDVLIDTCQGDDALPNGLDVTFE
Mmusculus  all identical  ENSMUSG00000022437  110VDVLIDTCHGEDALPNGLDVTF
Ggallus  all identical  ENSGALG00000014194  110VEVLIDTCQGDDALPNGLDVTF
Trubripes  all identical  ENSTRUG00000008882  111VEVLIDTSEGSDALPNGLDVT
Drerio  all identical  ENSDARG00000045814  110VEVVIDTAEGADALPNGLDVTF
Dmelanogaster  all identical  FBgn0033989  88VSVHIDVSRGADASPQGYEVTFK
Celegans  all conserved  C34E10.1  86SPSSN---EGYVVNFL
Xtropicalis  all identical  ENSXETG00000004871  66TCEGEDALPNGLDVTFE
protein features
start (aa)end (aa)featuredetails 
368372CONFLICTWAGGL -> LGRRW (in Ref. 1; AAD34046).might get lost (downstream of altered splice site)
371371CONFLICTMissing (in Ref. 8; AAH07830).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1410 / 1410
position (AA) of stopcodon in wt / mu AA sequence 470 / 470
position of stopcodon in wt / mu cDNA 1567 / 1567
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 158 / 158
chromosome 22
strand 1
last intron/exon boundary 1522
theoretical NMD boundary in CDS 1314
length of CDS 1410
coding sequence (CDS) position 329
cDNA position
(for ins/del: last normal base / first normal base)		 486
gDNA position
(for ins/del: last normal base / first normal base)		 16822
chromosomal position
(for ins/del: last normal base / first normal base)		 44368122
original gDNA sequence snippet ATTTTTTTATTTAGGTGATGACGCACTTCCAAATGGGTTAG
altered gDNA sequence snippet ATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGGGTTAG
original cDNA sequence snippet TGACACATGTCAAGGTGATGACGCACTTCCAAATGGGTTAG
altered cDNA sequence snippet TGACACATGTCAAGGTGATGGCGCACTTCCAAATGGGTTAG
wildtype AA sequence MGTVHARSLE PLPSSGPDFG GLGEEAEFVE VEPEAKQEIL ENKDVVVQHV HFDGLGRTKD
DIIICEIGDV FKAKNLIEVM RKSHEAREKL LRLGIFRQVD VLIDTCQGDD ALPNGLDVTF
EVTELRRLTG SYNTMVGNNE GSMVLGLKLP NLLGRAEKVT FQFSYGTKET SYGLSFFKPR
PGNFERNFSV NLYKVTGQFP WSSLRETDRG MSAEYSFPIW KTSHTVKWEG VWRELGCLSR
TASFAVRKES GHSLKSSLSH AMVIDSRNSS ILPRRGALLK VNQELAGYTG GDVSFIKEDF
ELQLNKQLIF DSVFSASFWG GMLVPIGDKP SSIADRFYLG GPTSIRGFSM HSIGPQSEGD
YLGGEAYWAG GLHLYTPLPF RPGQGGFGEL FRTHFFLNAG NLCNLNYGEG PKAHIRKLAE
CIRWSYGAGI VLRLGNIARL ELNYCVPMGV QTGDRICDGV QFGAGIRFL*
mutated AA sequence MGTVHARSLE PLPSSGPDFG GLGEEAEFVE VEPEAKQEIL ENKDVVVQHV HFDGLGRTKD
DIIICEIGDV FKAKNLIEVM RKSHEAREKL LRLGIFRQVD VLIDTCQGDG ALPNGLDVTF
EVTELRRLTG SYNTMVGNNE GSMVLGLKLP NLLGRAEKVT FQFSYGTKET SYGLSFFKPR
PGNFERNFSV NLYKVTGQFP WSSLRETDRG MSAEYSFPIW KTSHTVKWEG VWRELGCLSR
TASFAVRKES GHSLKSSLSH AMVIDSRNSS ILPRRGALLK VNQELAGYTG GDVSFIKEDF
ELQLNKQLIF DSVFSASFWG GMLVPIGDKP SSIADRFYLG GPTSIRGFSM HSIGPQSEGD
YLGGEAYWAG GLHLYTPLPF RPGQGGFGEL FRTHFFLNAG NLCNLNYGEG PKAHIRKLAE
CIRWSYGAGI VLRLGNIARL ELNYCVPMGV QTGDRICDGV QFGAGIRFL*
speed 0.69 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 9.26079376597508e-29 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:44368122A>GN/A show variant in all transcripts   IGV
HGNC symbol SAMM50
Ensembl transcript ID ENST00000396202
Genbank transcript ID N/A
UniProt peptide Q9Y512
alteration type single base exchange
alteration region intron
DNA changes g.16822A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3761472
databasehomozygous (G/G)heterozygousallele carriers
1000G1778691046
ExAC29881912322111
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9911
3.1371
(flanking)-0.3160.953
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -51) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased16816wt: 0.49 / mu: 0.55wt: TTTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAATG
mu: TTTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATG		 tagg|TGAT
Acc marginally increased16814wt: 0.9852 / mu: 0.9861 (marginal change - not scored)wt: TGTTTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAA
mu: TGTTTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAA		 ttta|GGTG
Acc marginally increased16819wt: 0.6583 / mu: 0.6617 (marginal change - not scored)wt: AATATTTTTTTATTTAGGTGATGACGCACTTCCAAATGGGT
mu: AATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGGGT		 gtga|TGAC
Acc marginally increased16815wt: 0.9832 / mu: 0.9868 (marginal change - not scored)wt: GTTTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAAT
mu: GTTTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAAT		 ttag|GTGA
Acc marginally increased16817wt: 0.2437 / mu: 0.2547 (marginal change - not scored)wt: TTAATATTTTTTTATTTAGGTGATGACGCACTTCCAAATGG
mu: TTAATATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGG		 aggt|GATG
distance from splice site 674
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
1010CONFLICTE -> G (in Ref. 5; BAD96377).might get lost (downstream of altered splice site)
368372CONFLICTWAGGL -> LGRRW (in Ref. 1; AAD34046).might get lost (downstream of altered splice site)
371371CONFLICTMissing (in Ref. 8; AAH07830).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 511 / 511
chromosome 22
strand 1
last intron/exon boundary 1245
theoretical NMD boundary in CDS 684
length of CDS 780
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 16822
chromosomal position
(for ins/del: last normal base / first normal base)		 44368122
original gDNA sequence snippet ATTTTTTTATTTAGGTGATGACGCACTTCCAAATGGGTTAG
altered gDNA sequence snippet ATTTTTTTATTTAGGTGATGGCGCACTTCCAAATGGGTTAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSAEYSFPIW KTSHTVKWEG VWRELGCLSR TASFAVRKES GHSLKSSLSH AMVIDSRNSS
ILPRRGALLK VNQELAGYTG GDVSFIKEDF ELQLNKQLIF DSVFSASFWG GMLVPIGDKP
SSIADRFYLG GPTSIRGFSM HSIGPQSEGD YLGGEAYWAG GLHLYTPLPF RPGQGGFGEL
FRTHFFLNAG NLCNLNYGEG PKAHIRKLAE CIRWSYGAGI VLRLGNIARL ELNYCVPMGV
QTGDRICDGV QFGAGIRFL*
mutated AA sequence N/A
speed 0.54 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
back to results table

Problems