Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000372887
Querying Taster for transcript #2: ENST00000372882
Querying Taster for transcript #3: ENST00000372874
Querying Taster for transcript #4: ENST00000537820
MT speed 0 s - this script 4.149431 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAdisease_causing_automatic0.999999997691003simple_aaeaffected0P273Qsingle base exchangers121908718show file
ADAdisease_causing_automatic0.999999999621134simple_aaeaffected0P297Qsingle base exchangers121908718show file
PKIGdisease_causing_automatic1without_aae0single base exchangers121908718show file
PKIGdisease_causing_automatic1without_aae0single base exchangers121908718show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997691003 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890002)
  • known disease mutation: rs1961 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249744G>TN/A show variant in all transcripts   IGV
HGNC symbol ADA
Ensembl transcript ID ENST00000537820
Genbank transcript ID N/A
UniProt peptide P00813
alteration type single base exchange
alteration region CDS
DNA changes c.818C>A
cDNA.902C>A
g.31131C>A
AA changes P273Q Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 273
frameshift no
known variant Reference ID: rs121908718
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1961 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5810
4.2580.999
(flanking)4.2271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained311260.39mu: ACAGATGACCAGCTC AGAT|gacc
distance from splice site 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      273DQANYSLNTDDPLIFKSTLDTDYQ
mutated  not conserved    273DQANYSLNTDDQLIFKSTLDTDY
Ptroglodytes  all identical  ENSPTRG00000013524  297DQANYSLNTDDPLIF
Mmulatta  all identical  ENSMMUG00000010603  297DQANYSLNTDDPLIF
Fcatus  all identical  ENSFCAG00000002474  330DQANYSLNTDDPLIF
Mmusculus  all identical  ENSMUSG00000017697  297DKANYSLNTDDPLIF
Ggallus  all identical  ENSGALG00000004170  295DQANYSINTDDPLIFNSNID
Trubripes  all identical  ENSTRUG00000010199  301DPLIFNSSLHLDY
Drerio  all identical  ENSDARG00000003113  299DKANYSLNTDDPTIFNST
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  330DDVNFSVSRDDPTCFD
Xtropicalis  all identical  ENSXETG00000003459  293DKANYSLNTDDPLIFGSTL
protein features
start (aa)end (aa)featuredetails 
270272STRANDmight get lost (downstream of altered splice site)
279285HELIXmight get lost (downstream of altered splice site)
290292STRANDmight get lost (downstream of altered splice site)
295295METALZinc; catalytic.might get lost (downstream of altered splice site)
296296BINDINGSubstrate.might get lost (downstream of altered splice site)
297300HELIXmight get lost (downstream of altered splice site)
304315HELIXmight get lost (downstream of altered splice site)
319331HELIXmight get lost (downstream of altered splice site)
333335STRANDmight get lost (downstream of altered splice site)
337351HELIXmight get lost (downstream of altered splice site)
340340CONFLICTK -> R (in Ref. 5; BAD97117).might get lost (downstream of altered splice site)
355362HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1020 / 1020
position (AA) of stopcodon in wt / mu AA sequence 340 / 340
position of stopcodon in wt / mu cDNA 1104 / 1104
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 85 / 85
chromosome 20
strand -1
last intron/exon boundary 1091
theoretical NMD boundary in CDS 956
length of CDS 1020
coding sequence (CDS) position 818
cDNA position
(for ins/del: last normal base / first normal base)		 902
gDNA position
(for ins/del: last normal base / first normal base)		 31131
chromosomal position
(for ins/del: last normal base / first normal base)		 43249744
original gDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered gDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
original cDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered cDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
wildtype AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
mutated AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDQLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 0.79 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

disease causing

 Model: simple_aae, prob: 0.999999999621134 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890002)
  • known disease mutation: rs1961 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249744G>TN/A show variant in all transcripts   IGV
HGNC symbol ADA
Ensembl transcript ID ENST00000372874
Genbank transcript ID NM_000022
UniProt peptide P00813
alteration type single base exchange
alteration region CDS
DNA changes c.890C>A
cDNA.1025C>A
g.31131C>A
AA changes P297Q Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 297
frameshift no
known variant Reference ID: rs121908718
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1961 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5810
4.2580.999
(flanking)4.2271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained311260.39mu: ACAGATGACCAGCTC AGAT|gacc
distance from splice site 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      297DQANYSLNTDDPLIFKSTLDTDYQ
mutated  not conserved    297DQANYSLNTDDQLIF
Ptroglodytes  all identical  ENSPTRG00000013524  297DQANYSLNTDDPLIF
Mmulatta  all identical  ENSMMUG00000010603  297DQANYSLNTDDPLIF
Fcatus  all identical  ENSFCAG00000002474  330DQANYSLNTDDPLIF
Mmusculus  all identical  ENSMUSG00000017697  297DKANYSLNTDDPLIF
Ggallus  all identical  ENSGALG00000004170  295DQANYSINTDDPLIFNSNID
Trubripes  all identical  ENSTRUG00000010199  301DPLIFNSSLHLDY
Drerio  all identical  ENSDARG00000003113  299DKANYSLNTDDPTIFNST
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  330DDVNFSVSRDDPTCFD
Xtropicalis  all identical  ENSXETG00000003459  293DKANYSLNTDDPLIFGSTL
protein features
start (aa)end (aa)featuredetails 
296296BINDINGSubstrate.might get lost (downstream of altered splice site)
297300HELIXlost
304315HELIXmight get lost (downstream of altered splice site)
319331HELIXmight get lost (downstream of altered splice site)
333335STRANDmight get lost (downstream of altered splice site)
337351HELIXmight get lost (downstream of altered splice site)
340340CONFLICTK -> R (in Ref. 5; BAD97117).might get lost (downstream of altered splice site)
355362HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1092 / 1092
position (AA) of stopcodon in wt / mu AA sequence 364 / 364
position of stopcodon in wt / mu cDNA 1227 / 1227
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 136 / 136
chromosome 20
strand -1
last intron/exon boundary 1214
theoretical NMD boundary in CDS 1028
length of CDS 1092
coding sequence (CDS) position 890
cDNA position
(for ins/del: last normal base / first normal base)		 1025
gDNA position
(for ins/del: last normal base / first normal base)		 31131
chromosomal position
(for ins/del: last normal base / first normal base)		 43249744
original gDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered gDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
original cDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered cDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
wildtype AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
mutated AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDQLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
speed 0.78 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

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM890002)
  • known disease mutation: rs1961 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249744G>TN/A show variant in all transcripts   IGV
HGNC symbol PKIG
Ensembl transcript ID ENST00000372882
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.89319G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908718
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1961 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5810
4.2580.999
(flanking)4.2271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 2830
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 144 / 144
chromosome 20
strand 1
last intron/exon boundary 295
theoretical NMD boundary in CDS 101
length of CDS 195
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)		 89319
chromosomal position
(for ins/del: last normal base / first normal base)		 43249744
original gDNA sequence snippet GGGTGGACTTGAAGATGAGCGGGTCATCTGTGTTGAGCGAG
altered gDNA sequence snippet GGGTGGACTTGAAGATGAGCTGGTCATCTGTGTTGAGCGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MMEVESSYSD FISCDRTGRR NAVPDIQGDS EAVSVRKLAG DMGELALEGA EMDLTMLPWL
VSNS*
mutated AA sequence N/A
speed 0.51 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

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM890002)
  • known disease mutation: rs1961 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249744G>TN/A show variant in all transcripts   IGV
HGNC symbol PKIG
Ensembl transcript ID ENST00000372887
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.89319G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908718
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1961 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5810
4.2580.999
(flanking)4.2271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 2830
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 304 / 304
chromosome 20
strand 1
last intron/exon boundary 455
theoretical NMD boundary in CDS 101
length of CDS 195
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)		 89319
chromosomal position
(for ins/del: last normal base / first normal base)		 43249744
original gDNA sequence snippet GGGTGGACTTGAAGATGAGCGGGTCATCTGTGTTGAGCGAG
altered gDNA sequence snippet GGGTGGACTTGAAGATGAGCTGGTCATCTGTGTTGAGCGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MMEVESSYSD FISCDRTGRR NAVPDIQGDS EAVSVRKLAG DMGELALEGA EMDLTMLPWL
VSNS*
mutated AA sequence N/A
speed 0.65 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