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 4.25834 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAdisease_causing_automatic0.999999978977467simple_aaeaffected0L152Msingle base exchangers121908728show file
ADAdisease_causing_automatic0.999999978977467simple_aaeaffected0L152Msingle base exchangers121908728show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999978977467 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970058)
  • known disease mutation: rs1979 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254234G>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.454C>A
cDNA.589C>A
g.26641C>A
AA changes L152M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs121908728
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01313

known disease mutation: rs1979 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency|Severe Combined Immune Deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7481
3.031
(flanking)2.6191
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased26644wt: 0.37 / mu: 0.45wt: TCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCC
mu: TCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAGCCC		 ctgt|GCTG
Donor gained266370.86mu: CGGTCCATCATGTGC GTCC|atca
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152ERDFGVKARSILCCMRHQPNWSPK
mutated  all conserved    152ERDFGVKARSIMCCMRHQPNWSP
Ptroglodytes  all identical  ENSPTRG00000013524  152ERDFGVKARSILCCMRHQPNWSP
Mmulatta  all identical  ENSMMUG00000010603  152ERDFGVKARSILCCMRHQPNWSL
Fcatus  all identical  ENSFCAG00000002474  185ERDFGVKVRSILCCMRHQPNWSL
Mmusculus  all identical  ENSMUSG00000017697  152EQAFGIKVRSILCCMRHQPSWSL
Ggallus  all identical  ENSGALG00000004170  153ERDFRIKARSILCCMRHMPSWSP
Trubripes  all identical  ENSTRUG00000010199  156ERAFNIKARSILCCMRHMPNWSM
Drerio  all identical  ENSDARG00000003113  155EQAFKTKARSILCCMRHMPNWSM
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  184EKQFGIKARSILCCIRGLDKKFP
Xtropicalis  all identical  ENSXETG00000003459  149EKAFNIKARSILCCMRHMPSWST
protein features
start (aa)end (aa)featuredetails 
147155STRANDlost
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 454
cDNA position
(for ins/del: last normal base / first normal base)		 589
gDNA position
(for ins/del: last normal base / first normal base)		 26641
chromosomal position
(for ins/del: last normal base / first normal base)		 43254234
original gDNA sequence snippet GGGTCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAG
altered gDNA sequence snippet GGGTCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAG
original cDNA sequence snippet GGGTCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAG
altered cDNA sequence snippet GGGTCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAG
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 IMCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
speed 0.72 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: 0.999999978977467 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970058)
  • known disease mutation: rs1979 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43254234G>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.454C>A
cDNA.538C>A
g.26641C>A
AA changes L152M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs121908728
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01313

known disease mutation: rs1979 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency|Severe Combined Immune Deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970058)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7481
3.031
(flanking)2.6191
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased26644wt: 0.37 / mu: 0.45wt: TCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAGCCC
mu: TCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAGCCC		 ctgt|GCTG
Donor gained266370.86mu: CGGTCCATCATGTGC GTCC|atca
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152ERDFGVKARSILCCMRHQPNWSPK
mutated  all conserved    152ERDFGVKARSIMCCMRHQPNWSP
Ptroglodytes  all identical  ENSPTRG00000013524  152ERDFGVKARSILCCMRHQPNWSP
Mmulatta  all identical  ENSMMUG00000010603  152ERDFGVKARSILCCMRHQPNWSL
Fcatus  all identical  ENSFCAG00000002474  185ERDFGVKVRSILCCMRHQPNWSL
Mmusculus  all identical  ENSMUSG00000017697  152EQAFGIKVRSILCCMRHQPSWSL
Ggallus  all identical  ENSGALG00000004170  153ERDFRIKARSILCCMRHMPSWSP
Trubripes  all identical  ENSTRUG00000010199  156ERAFNIKARSILCCMRHMPNWSM
Drerio  all identical  ENSDARG00000003113  155EQAFKTKARSILCCMRHMPNWSM
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  184EKQFGIKARSILCCIRGLDKKFP
Xtropicalis  all identical  ENSXETG00000003459  149EKAFNIKARSILCCMRHMPSWST
protein features
start (aa)end (aa)featuredetails 
147155STRANDlost
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 454
cDNA position
(for ins/del: last normal base / first normal base)		 538
gDNA position
(for ins/del: last normal base / first normal base)		 26641
chromosomal position
(for ins/del: last normal base / first normal base)		 43254234
original gDNA sequence snippet GGGTCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAG
altered gDNA sequence snippet GGGTCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAG
original cDNA sequence snippet GGGTCAAGGCCCGGTCCATCCTGTGCTGCATGCGCCACCAG
altered cDNA sequence snippet GGGTCAAGGCCCGGTCCATCATGTGCTGCATGCGCCACCAG
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 IMCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 0.86 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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