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 s - this script 4.318889 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAdisease_causing_automatic0.999999999997944simple_aaeaffected0R156Csingle base exchangers121908735show file
ADAdisease_causing_automatic0.999999999997944simple_aaeaffected0R156Csingle base exchangers121908735show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999997944 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920005)
  • known disease mutation: rs1970 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254222G>AN/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.466C>T
cDNA.601C>T
g.26653C>T
AA changes R156C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs121908735
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC033

known disease mutation: rs1970 (pathogenic for Severe combined immunodeficiency disease|Severe combined immunodeficiency due to ADA deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7331
4.0711
(flanking)4.1151
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased26649wt: 0.21 / mu: 0.25wt: GCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGA
mu: GCCCGGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGA		 ctgc|ATGC
Acc marginally increased26651wt: 0.8556 / mu: 0.9167 (marginal change - not scored)wt: CCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGT
mu: CCGGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGAGT		 gcat|GCGC
Acc marginally increased26660wt: 0.4950 / mu: 0.5411 (marginal change - not scored)wt: CCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGGATCACC
mu: CCTGTGCTGCATGTGCCACCAGCCCAGTGAGTAGGATCACC		 acca|GCCC
Acc marginally increased26644wt: 0.3680 / mu: 0.4017 (marginal change - not scored)wt: TCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCC
mu: TCAAGGCCCGGTCCATCCTGTGCTGCATGTGCCACCAGCCC		 ctgt|GCTG
Donor gained266460.47mu: CTGTGCTGCATGTGC GTGC|tgca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156GVKARSILCCMRHQPNWSPKVVEL
mutated  not conserved    156GVKARSILCCMCHQPNWSPKVVE
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
start (aa)end (aa)featuredetails 
147155STRANDmight get lost (downstream of altered splice site)
159161HELIXmight get lost (downstream of altered splice site)
162171HELIXmight get lost (downstream of altered splice site)
172176TURNmight get lost (downstream of altered splice site)
177184STRANDmight get lost (downstream of altered splice site)
184184BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
191193HELIXmight get lost (downstream of altered splice site)
195207HELIXmight get lost (downstream of altered splice site)
210219STRANDmight get lost (downstream of altered splice site)
214214METALZinc; catalytic.might get lost (downstream of altered splice site)
217217ACT_SITEProton donor (Probable).might get lost (downstream of altered splice site)
221229HELIXmight get lost (downstream of altered splice site)
232232MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
234238STRANDmight get lost (downstream of altered splice site)
238238SITEImportant for catalytic activity (By similarity).might get lost (downstream of altered splice site)
240244HELIXmight get lost (downstream of altered splice site)
246254HELIXmight get lost (downstream of altered splice site)
258261STRANDmight get lost (downstream of altered splice site)
263268HELIXmight get lost (downstream of altered splice site)
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 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 466
cDNA position
(for ins/del: last normal base / first normal base)		 601
gDNA position
(for ins/del: last normal base / first normal base)		 26653
chromosomal position
(for ins/del: last normal base / first normal base)		 43254222
original gDNA sequence snippet GGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAG
altered gDNA sequence snippet GGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGAGTAG
original cDNA sequence snippet GGTCCATCCTGTGCTGCATGCGCCACCAGCCCAACTGGTCC
altered cDNA sequence snippet GGTCCATCCTGTGCTGCATGTGCCACCAGCCCAACTGGTCC
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 ILCCMCHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
speed 1.17 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: 0.999999999997944 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920005)
  • known disease mutation: rs1970 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254222G>AN/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.466C>T
cDNA.550C>T
g.26653C>T
AA changes R156C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs121908735
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC033

known disease mutation: rs1970 (pathogenic for Severe combined immunodeficiency disease|Severe combined immunodeficiency due to ADA deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920005)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7331
4.0711
(flanking)4.1151
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased26649wt: 0.21 / mu: 0.25wt: GCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGA
mu: GCCCGGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGA		 ctgc|ATGC
Acc marginally increased26651wt: 0.8556 / mu: 0.9167 (marginal change - not scored)wt: CCGGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGT
mu: CCGGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGAGT		 gcat|GCGC
Acc marginally increased26660wt: 0.4950 / mu: 0.5411 (marginal change - not scored)wt: CCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAGGATCACC
mu: CCTGTGCTGCATGTGCCACCAGCCCAGTGAGTAGGATCACC		 acca|GCCC
Acc marginally increased26644wt: 0.3680 / mu: 0.4017 (marginal change - not scored)wt: TCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCC
mu: TCAAGGCCCGGTCCATCCTGTGCTGCATGTGCCACCAGCCC		 ctgt|GCTG
Donor gained266460.47mu: CTGTGCTGCATGTGC GTGC|tgca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156GVKARSILCCMRHQPNWSPKVVEL
mutated  not conserved    156GVKARSILCCMCHQPNWSPKVVE
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
start (aa)end (aa)featuredetails 
147155STRANDmight get lost (downstream of altered splice site)
159161HELIXmight get lost (downstream of altered splice site)
162171HELIXmight get lost (downstream of altered splice site)
172176TURNmight get lost (downstream of altered splice site)
177184STRANDmight get lost (downstream of altered splice site)
184184BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
191193HELIXmight get lost (downstream of altered splice site)
195207HELIXmight get lost (downstream of altered splice site)
210219STRANDmight get lost (downstream of altered splice site)
214214METALZinc; catalytic.might get lost (downstream of altered splice site)
217217ACT_SITEProton donor (Probable).might get lost (downstream of altered splice site)
221229HELIXmight get lost (downstream of altered splice site)
232232MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
234238STRANDmight get lost (downstream of altered splice site)
238238SITEImportant for catalytic activity (By similarity).might get lost (downstream of altered splice site)
240244HELIXmight get lost (downstream of altered splice site)
246254HELIXmight get lost (downstream of altered splice site)
258261STRANDmight get lost (downstream of altered splice site)
263268HELIXmight get lost (downstream of altered splice site)
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 466
cDNA position
(for ins/del: last normal base / first normal base)		 550
gDNA position
(for ins/del: last normal base / first normal base)		 26653
chromosomal position
(for ins/del: last normal base / first normal base)		 43254222
original gDNA sequence snippet GGTCCATCCTGTGCTGCATGCGCCACCAGCCCAGTGAGTAG
altered gDNA sequence snippet GGTCCATCCTGTGCTGCATGTGCCACCAGCCCAGTGAGTAG
original cDNA sequence snippet GGTCCATCCTGTGCTGCATGCGCCACCAGCCCAACTGGTCC
altered cDNA sequence snippet GGTCCATCCTGTGCTGCATGTGCCACCAGCCCAACTGGTCC
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 ILCCMCHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 1.15 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

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