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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000372874
Querying Taster for transcript #2: ENST00000537820
MT speed 0.39 s - this script 2.606048 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAdisease_causing_automatic0.999999999919287simple_aae0R156Hsingle base exchangers121908722show file
ADAdisease_causing_automatic0.999999999919287simple_aae0R156Hsingle base exchangers121908722show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999919287 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM109816)
  • known disease mutation at this position (HGMD CM930009)
  • known disease mutation: rs1984 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254221C>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.467G>A
cDNA.551G>A
g.26654G>A
AA changes R156H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs121908722
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1984 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|SCID due to ADA deficiency, delayed onset|Severe Combined Immune Deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1131
5.7331
(flanking)4.0711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased26651wt: 0.8556 / mu: 0.8764 (marginal change - not scored)wt: CCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGT
mu: CCGGTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGAGT		 gcat|GCGC
Acc marginally increased26660wt: 0.4950 / mu: 0.5425 (marginal change - not scored)wt: CCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGGATCACC
mu: CCTGTGCTGCATGCACCACCAGCCCAGTGAGTAGGATCACC		 acca|GCCC
Acc marginally increased26649wt: 0.2123 / mu: 0.2159 (marginal change - not scored)wt: GCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGA
mu: GCCCGGTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGA		 ctgc|ATGC
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156GVKARSILCCMRHQPNWSPKVVEL
mutated  not conserved    156GVKARSILCCMHHQPNWSPKVVE
Ptroglodytes  all identical  ENSPTRG00000013524  156GVKARSILCCMRHQPNWSPEVVE
Mmulatta  all identical  ENSMMUG00000010603  156GVKARSILCCMRHQPNWSLEVVE
Fcatus  all identical  ENSFCAG00000002474  189GVKVRSILCCMRHQPNWSLEVVE
Mmusculus  all identical  ENSMUSG00000017697  156GIKVRSILCCMRHQPSWSLEVLE
Ggallus  all identical  ENSGALG00000004170  157RIKARSILCCMRHMPSWSPEVVE
Trubripes  all identical  ENSTRUG00000010199  160NIKARSILCCMRHMPNWSMDIVE
Drerio  all identical  ENSDARG00000003113  159KTKARSILCCMRHMPNWSMEVVE
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  188GIKARSILCCIRGLDKKFPQLILD
Xtropicalis  all identical  ENSXETG00000003459  153NIKARSILCCMRHMPSWSTEVVE
protein features no protein features affected
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 467
cDNA position
(for ins/del: last normal base / first normal base)		 551
gDNA position
(for ins/del: last normal base / first normal base)		 26654
chromosomal position
(for ins/del: last normal base / first normal base)		 43254221
original gDNA sequence snippet GTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGG
altered gDNA sequence snippet GTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGAGTAGG
original cDNA sequence snippet GTCCATCCTGTGCTGCATGCGCCACCAGCCCAACTGGTCCC
altered cDNA sequence snippet GTCCATCCTGTGCTGCATGCACCACCAGCCCAACTGGTCCC
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 ILCCMHHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 0.17 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: 0.999999999919287 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM109816)
  • known disease mutation at this position (HGMD CM930009)
  • known disease mutation: rs1984 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254221C>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.467G>A
cDNA.602G>A
g.26654G>A
AA changes R156H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs121908722
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1984 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|SCID due to ADA deficiency, delayed onset|Severe Combined Immune Deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM109816)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930009)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1131
5.7331
(flanking)4.0711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased26651wt: 0.8556 / mu: 0.8764 (marginal change - not scored)wt: CCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGT
mu: CCGGTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGAGT		 gcat|GCGC
Acc marginally increased26660wt: 0.4950 / mu: 0.5425 (marginal change - not scored)wt: CCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGGATCACC
mu: CCTGTGCTGCATGCACCACCAGCCCAGTGAGTAGGATCACC		 acca|GCCC
Acc marginally increased26649wt: 0.2123 / mu: 0.2159 (marginal change - not scored)wt: GCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGA
mu: GCCCGGTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGA		 ctgc|ATGC
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156GVKARSILCCMRHQPNWSPKVVEL
mutated  not conserved    156GVKARSILCCMHHQPNWSPKVVE
Ptroglodytes  all identical  ENSPTRG00000013524  156GVKARSILCCMRHQPNWSPEVVE
Mmulatta  all identical  ENSMMUG00000010603  156GVKARSILCCMRHQPNWSLEVVE
Fcatus  all identical  ENSFCAG00000002474  189GVKVRSILCCMRHQPNWSLEVVE
Mmusculus  all identical  ENSMUSG00000017697  156GIKVRSILCCMRHQPSWSLEVLE
Ggallus  all identical  ENSGALG00000004170  157RIKARSILCCMRHMPSWSPEVVE
Trubripes  all identical  ENSTRUG00000010199  160NIKARSILCCMRHMPNWSMDIVE
Drerio  all identical  ENSDARG00000003113  159KTKARSILCCMRHMPNWSMEVVE
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  188GIKARSILCCIRGLDKKFPQLILD
Xtropicalis  all identical  ENSXETG00000003459  153NIKARSILCCMRHMPSWSTEVVE
protein features no protein features affected
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 467
cDNA position
(for ins/del: last normal base / first normal base)		 602
gDNA position
(for ins/del: last normal base / first normal base)		 26654
chromosomal position
(for ins/del: last normal base / first normal base)		 43254221
original gDNA sequence snippet GTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGG
altered gDNA sequence snippet GTCCATCCTGTGCTGCATGCACCACCAGCCCAGTGAGTAGG
original cDNA sequence snippet GTCCATCCTGTGCTGCATGCGCCACCAGCCCAACTGGTCCC
altered cDNA sequence snippet GTCCATCCTGTGCTGCATGCACCACCAGCCCAACTGGTCCC
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 ILCCMHHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
speed 0.22 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