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 3.814897 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAdisease_causing_automatic0.999999987111312simple_aae0A329Vsingle base exchangers121908715show file
ADAdisease_causing_automatic0.999999987111312simple_aae0A305Vsingle base exchangers121908715show file
PKIGdisease_causing_automatic1without_aaeaffected0single base exchangers121908715show file
PKIGdisease_causing_automatic1without_aaeaffected0single base exchangers121908715show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999987111312 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM870001)
  • known disease mutation: rs1959 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249032G>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.986C>T
cDNA.1121C>T
g.31843C>T
AA changes A329V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 329
frameshift no
known variant Reference ID: rs121908715
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC099

known disease mutation: rs1959 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.8730.003
3.9250.996
(flanking)1.7140.997
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 increased31833wt: 0.2697 / mu: 0.3019 (marginal change - not scored)wt: TGCCATTCTGGCCTTTCCAGAACATCAATGCGGCCAAATCT
mu: TGCCATTCTGGCCTTTCCAGAACATCAATGTGGCCAAATCT		 caga|ACAT
Donor marginally increased31836wt: 0.8762 / mu: 0.9597 (marginal change - not scored)wt: AGAACATCAATGCGG
mu: AGAACATCAATGTGG		 AACA|tcaa
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      329TEEEFKRLNINAAKSSFLPEDEKR
mutated  not conserved    329TEEEFKRLNINVAKSSFLPEDEK
Ptroglodytes  all identical  ENSPTRG00000013524  329TEEEFKRLNINAAKSSFLPEDEK
Mmulatta  all identical  ENSMMUG00000010603  329TEEEFKRLNINAAKSSFLPEDEK
Fcatus  all identical  ENSFCAG00000002474  361TEEEFKRLNINAAKSSFLPEDEK
Mmusculus  all identical  ENSMUSG00000017697  329TEEEFKRLNINAAKSSFLPEEEK
Ggallus  all identical  ENSGALG00000004170  328TEEDFKRVNINAAQSSFLPEKEK
Trubripes  all identical  ENSTRUG00000010199  333TEQEFKRLNINAAESCFLPEKEK
Drerio  all identical  ENSDARG00000003113  332TEEEFKRLNINAAKSCFLPEKEK
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  365DVHQLWKAQLNAARSCFLPEDEK
Xtropicalis  all identical  ENSXETG00000003459  326TEEEFKRVNINAAKSSFLPESEK
protein features
start (aa)end (aa)featuredetails 
319331HELIXlost
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 986
cDNA position
(for ins/del: last normal base / first normal base)		 1121
gDNA position
(for ins/del: last normal base / first normal base)		 31843
chromosomal position
(for ins/del: last normal base / first normal base)		 43249032
original gDNA sequence snippet GCCTTTCCAGAACATCAATGCGGCCAAATCTAGTTTCCTCC
altered gDNA sequence snippet GCCTTTCCAGAACATCAATGTGGCCAAATCTAGTTTCCTCC
original cDNA sequence snippet TAAAAGGCTGAACATCAATGCGGCCAAATCTAGTTTCCTCC
altered cDNA sequence snippet TAAAAGGCTGAACATCAATGTGGCCAAATCTAGTTTCCTCC
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 SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINVA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*
speed 0.92 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: 0.999999987111312 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM870001)
  • known disease mutation: rs1959 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249032G>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.914C>T
cDNA.998C>T
g.31843C>T
AA changes A305V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 305
frameshift no
known variant Reference ID: rs121908715
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC099

known disease mutation: rs1959 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.8730.003
3.9250.996
(flanking)1.7140.997
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 increased31833wt: 0.2697 / mu: 0.3019 (marginal change - not scored)wt: TGCCATTCTGGCCTTTCCAGAACATCAATGCGGCCAAATCT
mu: TGCCATTCTGGCCTTTCCAGAACATCAATGTGGCCAAATCT		 caga|ACAT
Donor marginally increased31836wt: 0.8762 / mu: 0.9597 (marginal change - not scored)wt: AGAACATCAATGCGG
mu: AGAACATCAATGTGG		 AACA|tcaa
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      305TEEEFKRLNINAAKSSFLPEDEKR
mutated  not conserved    305LNINVAKSSFLPEDEK
Ptroglodytes  all identical  ENSPTRG00000013524  329TEEEFKRLNINAAKSSFLPEDEK
Mmulatta  all identical  ENSMMUG00000010603  329TEEEFKRLNINAAKSSFLPEDEK
Fcatus  all identical  ENSFCAG00000002474  361TEEEFKRLNINAAKSSFLPEDEK
Mmusculus  all identical  ENSMUSG00000017697  329TEEEFKRLNINAAKSSFLPEEEK
Ggallus  all identical  ENSGALG00000004170  328TEEDFKRVNINAAQSSFLPEKEK
Trubripes  all identical  ENSTRUG00000010199  333TEQEFKRLNINAAESCFLPEKEK
Drerio  all identical  ENSDARG00000003113  332TEEEFKRLNINAAKSCFLPEKEK
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  365DVHQLWKAQLNAARSCFLPEDEK
Xtropicalis  all identical  ENSXETG00000003459  326TEEEFKRVNINAAKSSFLPESEK
protein features
start (aa)end (aa)featuredetails 
304315HELIXlost
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 914
cDNA position
(for ins/del: last normal base / first normal base)		 998
gDNA position
(for ins/del: last normal base / first normal base)		 31843
chromosomal position
(for ins/del: last normal base / first normal base)		 43249032
original gDNA sequence snippet GCCTTTCCAGAACATCAATGCGGCCAAATCTAGTTTCCTCC
altered gDNA sequence snippet GCCTTTCCAGAACATCAATGTGGCCAAATCTAGTTTCCTCC
original cDNA sequence snippet TAAAAGGCTGAACATCAATGCGGCCAAATCTAGTTTCCTCC
altered cDNA sequence snippet TAAAAGGCTGAACATCAATGTGGCCAAATCTAGTTTCCTCC
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 DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINVAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 0.19 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 CM870001)
  • known disease mutation: rs1959 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249032G>AN/A show variant in all transcripts   IGV
HGNC symbol PKIG
Ensembl transcript ID ENST00000372887
Genbank transcript ID N/A
UniProt peptide Q9Y2B9
alteration type single base exchange
alteration region intron
DNA changes g.88607G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908715
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC099

known disease mutation: rs1959 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.8730.003
3.9250.996
(flanking)1.7140.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased88609wt: 0.9725 / mu: 0.9815 (marginal change - not scored)wt: GCCGCATTGATGTTC
mu: GCCACATTGATGTTC		 CGCA|ttga
Donor gained886030.43mu: GATTTGGCCACATTG TTTG|gcca
distance from splice site 3542
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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)		 88607
chromosomal position
(for ins/del: last normal base / first normal base)		 43249032
original gDNA sequence snippet GGAGGAAACTAGATTTGGCCGCATTGATGTTCTGGAAAGGC
altered gDNA sequence snippet GGAGGAAACTAGATTTGGCCACATTGATGTTCTGGAAAGGC
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 0.73 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 CM870001)
  • known disease mutation: rs1959 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249032G>AN/A show variant in all transcripts   IGV
HGNC symbol PKIG
Ensembl transcript ID ENST00000372882
Genbank transcript ID N/A
UniProt peptide Q9Y2B9
alteration type single base exchange
alteration region intron
DNA changes g.88607G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908715
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC099

known disease mutation: rs1959 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870001)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.8730.003
3.9250.996
(flanking)1.7140.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased88609wt: 0.9725 / mu: 0.9815 (marginal change - not scored)wt: GCCGCATTGATGTTC
mu: GCCACATTGATGTTC		 CGCA|ttga
Donor gained886030.43mu: GATTTGGCCACATTG TTTG|gcca
distance from splice site 3542
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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)		 88607
chromosomal position
(for ins/del: last normal base / first normal base)		 43249032
original gDNA sequence snippet GGAGGAAACTAGATTTGGCCGCATTGATGTTCTGGAAAGGC
altered gDNA sequence snippet GGAGGAAACTAGATTTGGCCACATTGATGTTCTGGAAAGGC
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 0.17 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

Problems