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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000360786
Querying Taster for transcript #2: ENST00000454994
Querying Taster for transcript #3: ENST00000357771
MT speed 0 s - this script 3.517773 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJA9polymorphism_automatic4.38982183936787e-13simple_aaeaffectedV497Isingle base exchangers880303show file
GJA9polymorphism_automatic4.38982183936787e-13simple_aaeaffectedV497Isingle base exchangers880303show file
GJA9polymorphism_automatic3.55960158016089e-07without_aaeaffectedsingle base exchangers880303show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999561 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:39340282C>TN/A show variant in all transcripts   IGV
HGNC symbol GJA9
Ensembl transcript ID ENST00000360786
Genbank transcript ID N/A
UniProt peptide P57773
alteration type single base exchange
alteration region CDS
DNA changes c.1489G>A
cDNA.1742G>A
g.7008G>A
AA changes V497I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 497
frameshift no
known variant Reference ID: rs880303
databasehomozygous (T/T)heterozygousallele carriers
1000G2869851271
ExAC100301270722737
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1510.003
-0.3210
(flanking)-1.9820
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 increased7009wt: 0.2914 / mu: 0.3037 (marginal change - not scored)wt: TGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAATC
mu: TGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAATC		 acgt|AGTG
Acc increased7005wt: 0.22 / mu: 0.31wt: ATCCTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAAC
mu: ATCCTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAAC		 aatc|ACGT
Donor marginally increased7005wt: 0.6876 / mu: 0.7541 (marginal change - not scored)wt: CAAATCACGTAGTGT
mu: CAAATCACATAGTGT		 AATC|acgt
distance from splice site 160
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      497TCNNPVCPPNHVVSLTNNLIGRRV
mutated  all conserved    497TCNNPVCPPNHIVSLTNNLIGRR
Ptroglodytes  all identical  ENSPTRG00000034043  497TCNNPVCPPNHVVSLTNNLIGRR
Mmulatta  all identical  ENSMMUG00000010135  497TCNNPVCPPNHVVSLTNNLIGRR
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000009230  n/a
Drerio  no alignment  ENSDARG00000086453  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000005268  501TCEGSVTFSPSRRMSLASNASSRR
protein features
start (aa)end (aa)featuredetails 
231515TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1548 / 1548
position (AA) of stopcodon in wt / mu AA sequence 516 / 516
position of stopcodon in wt / mu cDNA 1801 / 1801
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 254 / 254
chromosome 1
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1548
coding sequence (CDS) position 1489
cDNA position
(for ins/del: last normal base / first normal base)		 1742
gDNA position
(for ins/del: last normal base / first normal base)		 7008
chromosomal position
(for ins/del: last normal base / first normal base)		 39340282
original gDNA sequence snippet CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT
altered gDNA sequence snippet CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT
original cDNA sequence snippet CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT
altered cDNA sequence snippet CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT
wildtype AA sequence MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK GNLKGQFRKG TVRTLPPSQG DSQSLDIPNT ADSLGGLSFE
PGLVRTCNNP VCPPNHVVSL TNNLIGRRVP TDLQI*
mutated AA sequence MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK GNLKGQFRKG TVRTLPPSQG DSQSLDIPNT ADSLGGLSFE
PGLVRTCNNP VCPPNHIVSL TNNLIGRRVP TDLQI*
speed 0.71 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

polymorphism

 Model: simple_aae, prob: 0.999999999999561 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:39340282C>TN/A show variant in all transcripts   IGV
HGNC symbol GJA9
Ensembl transcript ID ENST00000357771
Genbank transcript ID NM_030772
UniProt peptide P57773
alteration type single base exchange
alteration region CDS
DNA changes c.1489G>A
cDNA.1770G>A
g.7008G>A
AA changes V497I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 497
frameshift no
known variant Reference ID: rs880303
databasehomozygous (T/T)heterozygousallele carriers
1000G2869851271
ExAC100301270722737
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1510.003
-0.3210
(flanking)-1.9820
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 increased7009wt: 0.2914 / mu: 0.3037 (marginal change - not scored)wt: TGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAATC
mu: TGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAATC		 acgt|AGTG
Acc increased7005wt: 0.22 / mu: 0.31wt: ATCCTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAAC
mu: ATCCTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAAC		 aatc|ACGT
Donor marginally increased7005wt: 0.6876 / mu: 0.7541 (marginal change - not scored)wt: CAAATCACGTAGTGT
mu: CAAATCACATAGTGT		 AATC|acgt
distance from splice site 544
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      497TCNNPVCPPNHVVSLTNNLIGRRV
mutated  all conserved    497TCNNPVCPPNHIVSLTNNLIGRR
Ptroglodytes  all identical  ENSPTRG00000034043  497TCNNPVCPPNHVVSLTNNLIGRR
Mmulatta  all identical  ENSMMUG00000010135  497TCNNPVCPPNHVVSLTNNLIGRR
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000009230  n/a
Drerio  no alignment  ENSDARG00000086453  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000005268  501TCEGSVTFSPSRRMSLASNASSRR
protein features
start (aa)end (aa)featuredetails 
231515TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1548 / 1548
position (AA) of stopcodon in wt / mu AA sequence 516 / 516
position of stopcodon in wt / mu cDNA 1829 / 1829
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 282 / 282
chromosome 1
strand -1
last intron/exon boundary 187
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1548
coding sequence (CDS) position 1489
cDNA position
(for ins/del: last normal base / first normal base)		 1770
gDNA position
(for ins/del: last normal base / first normal base)		 7008
chromosomal position
(for ins/del: last normal base / first normal base)		 39340282
original gDNA sequence snippet CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT
altered gDNA sequence snippet CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT
original cDNA sequence snippet CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT
altered cDNA sequence snippet CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT
wildtype AA sequence MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK GNLKGQFRKG TVRTLPPSQG DSQSLDIPNT ADSLGGLSFE
PGLVRTCNNP VCPPNHVVSL TNNLIGRRVP TDLQI*
mutated AA sequence MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK GNLKGQFRKG TVRTLPPSQG DSQSLDIPNT ADSLGGLSFE
PGLVRTCNNP VCPPNHIVSL TNNLIGRRVP TDLQI*
speed 0.81 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

polymorphism

 Model: without_aae, prob: 0.999999644039842 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:39340282C>TN/A show variant in all transcripts   IGV
HGNC symbol GJA9
Ensembl transcript ID ENST00000454994
Genbank transcript ID N/A
UniProt peptide P57773
alteration type single base exchange
alteration region intron
DNA changes g.7008G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs880303
databasehomozygous (T/T)heterozygousallele carriers
1000G2869851271
ExAC100301270722737
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1510.003
-0.3210
(flanking)-1.9820
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 increased7009wt: 0.2914 / mu: 0.3037 (marginal change - not scored)wt: TGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAATC
mu: TGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAATC		 acgt|AGTG
Acc increased7005wt: 0.22 / mu: 0.31wt: ATCCTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAAC
mu: ATCCTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAAC		 aatc|ACGT
Donor marginally increased7005wt: 0.6876 / mu: 0.7541 (marginal change - not scored)wt: CAAATCACGTAGTGT
mu: CAAATCACATAGTGT		 AATC|acgt
distance from splice site 168
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
231515TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
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 278 / 278
chromosome 1
strand -1
last intron/exon boundary 2166
theoretical NMD boundary in CDS 1838
length of CDS 1545
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)		 7008
chromosomal position
(for ins/del: last normal base / first normal base)		 39340282
original gDNA sequence snippet CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT
altered gDNA sequence snippet CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK VPGSKATASS LLLILQRPTS SQPRLKETPK IKAEAKIYDS
KHPPRLLQST VSTFSGREPR SPAPMGHHSF RGPR*
mutated AA sequence N/A
speed 0.66 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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