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: ENST00000287652
Querying Taster for transcript #2: ENST00000448281
MT speed 2.88 s - this script 8.3305 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TATDN2polymorphism_automatic9.99200722162641e-15simple_aaeaffectedV256Isingle base exchangers394558show file
TATDN2polymorphism_automatic9.99200722162641e-15simple_aaeaffectedV256Isingle base exchangers394558show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999999 (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) chr3:10302172G>AN/A show variant in all transcripts   IGV
HGNC symbol TATDN2
Ensembl transcript ID ENST00000287652
Genbank transcript ID N/A
UniProt peptide Q93075
alteration type single base exchange
alteration region CDS
DNA changes c.766G>A
cDNA.1817G>A
g.12466G>A
AA changes V256I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
256
frameshift no
known variant Reference ID: rs394558
databasehomozygous (A/A)heterozygousallele carriers
1000G10578721929
ExAC17500-223315267
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4310.007
-0.040.001
(flanking)-0.0850
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 increased12459wt: 0.8678 / mu: 0.9105 (marginal change - not scored)wt: GCAACCCCAGAGGTC
mu: GCAACCCCAGAGATC
 AACC|ccag
Donor increased12469wt: 0.44 / mu: 0.70wt: AGGTCAGCATGGAGG
mu: AGATCAGCATGGAGG
 GTCA|gcat
Donor increased12462wt: 0.24 / mu: 0.67wt: ACCCCAGAGGTCAGC
mu: ACCCCAGAGATCAGC
 CCCA|gagg
Donor increased12471wt: 0.23 / mu: 0.48wt: GTCAGCATGGAGGAG
mu: ATCAGCATGGAGGAG
 CAGC|atgg
Donor increased12464wt: 0.85 / mu: 0.95wt: CCCAGAGGTCAGCAT
mu: CCCAGAGATCAGCAT
 CAGA|ggtc
distance from splice site 183
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      256AAQKEKDATPEVSMEEDKTVPERS
mutated  all conserved    256AAQKEKDATPEISMEEDKTVPER
Ptroglodytes  all conserved  ENSPTRG00000014616  256AAQKEKDSTPEISVEEDKTVPER
Mmulatta  all conserved  ENSMMUG00000019933  257TAQKEKDSTPEISVEEDKTVPEK
Fcatus  all identical  ENSFCAG00000011241  251PPQKGKESAPEVRAEEEKAVLER
Mmusculus  all identical  ENSMUSG00000056952  267VSQKEESHT-KVSVEKEASALDR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000070618  201AEEEEKHSDLECCSFSEKNNPS-
Dmelanogaster  no homologue    
Celegans  no alignment  Y37H2A.1  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
420420MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
499499METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
501501METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
593593METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
593593METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
630630METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
655655METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
707707METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2286 / 2286
position (AA) of stopcodon in wt / mu AA sequence 762 / 762
position of stopcodon in wt / mu cDNA 3337 / 3337
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 1052 / 1052
chromosome 3
strand 1
last intron/exon boundary 3347
theoretical NMD boundary in CDS 2245
length of CDS 2286
coding sequence (CDS) position 766
cDNA position
(for ins/del: last normal base / first normal base)
1817
gDNA position
(for ins/del: last normal base / first normal base)
12466
chromosomal position
(for ins/del: last normal base / first normal base)
10302172
original gDNA sequence snippet AGAAAGACGCAACCCCAGAGGTCAGCATGGAGGAGGATAAG
altered gDNA sequence snippet AGAAAGACGCAACCCCAGAGATCAGCATGGAGGAGGATAAG
original cDNA sequence snippet AGAAAGACGCAACCCCAGAGGTCAGCATGGAGGAGGATAAG
altered cDNA sequence snippet AGAAAGACGCAACCCCAGAGATCAGCATGGAGGAGGATAAG
wildtype AA sequence MASERGKVKH NWSSTSEGCP RKRSCLREPC DVAPSSRPAQ RSASRSGGPS SPKRLKAQKE
DDVACSRRLS WGSSRRRNNS SSSFSPHFLG PGVGGAASKG CLIRNTRGFL SSGGSPLRPA
NASLEEMASL EEEACSLKVD SKDSSHNSTN SEFAAEAEGQ NDTIEEPNKV QKRKRDRLRD
QGSTMIYLKA IQGILGKSMP KRKGEAATRA KPSAAEHPSH GEGPARSEGP AKTAEGAARS
VTVTAAQKEK DATPEVSMEE DKTVPERSSF YDRRVVIDPQ EKPSEEPLGD RRTVIDKCSP
PLEFLDDSDS HLEIQKHKDR EVVMEHPSSG SDWSDVEEIS TVRFSQEEPV SLKPSAVPEP
SSFTTDYVMY PPHLYSSPWC DYASYWTSSP KPSSYPSTGS SSNDAAQVGK SSRSRMSDYS
PNSTGSVQNT SRDMEASEEG WSQNSRSFRF SRSSEEREVK EKRTFQEEMP PRPCGGHASS
SLPKSHLEPS LEEGFIDTHC HLDMLYSKLS FQGTFTKFRK IYSSSFPKEF QGCISDFCDP
RTLTDCLWEE LLKEDLVWGA FGCHPHFARY YSESQERNLL QALRHPKAVA FGEMGLDYSY
KCTTPVPEQH KVFERQLQLA VSLKKPLVIH CREADEDLLE IMKKFVPPDY KIHRHCFTGS
YPVIEPLLKY FPNMSVGFTA VLTYSSAWEA REALRQIPLE RIIVETDAPY FLPRQVPKSL
CQYAHPGLAL HTVREIARVK DQPLSLTLAA LRENTSRLYS L*
mutated AA sequence MASERGKVKH NWSSTSEGCP RKRSCLREPC DVAPSSRPAQ RSASRSGGPS SPKRLKAQKE
DDVACSRRLS WGSSRRRNNS SSSFSPHFLG PGVGGAASKG CLIRNTRGFL SSGGSPLRPA
NASLEEMASL EEEACSLKVD SKDSSHNSTN SEFAAEAEGQ NDTIEEPNKV QKRKRDRLRD
QGSTMIYLKA IQGILGKSMP KRKGEAATRA KPSAAEHPSH GEGPARSEGP AKTAEGAARS
VTVTAAQKEK DATPEISMEE DKTVPERSSF YDRRVVIDPQ EKPSEEPLGD RRTVIDKCSP
PLEFLDDSDS HLEIQKHKDR EVVMEHPSSG SDWSDVEEIS TVRFSQEEPV SLKPSAVPEP
SSFTTDYVMY PPHLYSSPWC DYASYWTSSP KPSSYPSTGS SSNDAAQVGK SSRSRMSDYS
PNSTGSVQNT SRDMEASEEG WSQNSRSFRF SRSSEEREVK EKRTFQEEMP PRPCGGHASS
SLPKSHLEPS LEEGFIDTHC HLDMLYSKLS FQGTFTKFRK IYSSSFPKEF QGCISDFCDP
RTLTDCLWEE LLKEDLVWGA FGCHPHFARY YSESQERNLL QALRHPKAVA FGEMGLDYSY
KCTTPVPEQH KVFERQLQLA VSLKKPLVIH CREADEDLLE IMKKFVPPDY KIHRHCFTGS
YPVIEPLLKY FPNMSVGFTA VLTYSSAWEA REALRQIPLE RIIVETDAPY FLPRQVPKSL
CQYAHPGLAL HTVREIARVK DQPLSLTLAA LRENTSRLYS L*
speed 1.70 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: 0.99999999999999 (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) chr3:10302172G>AN/A show variant in all transcripts   IGV
HGNC symbol TATDN2
Ensembl transcript ID ENST00000448281
Genbank transcript ID NM_014760
UniProt peptide Q93075
alteration type single base exchange
alteration region CDS
DNA changes c.766G>A
cDNA.928G>A
g.12466G>A
AA changes V256I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
256
frameshift no
known variant Reference ID: rs394558
databasehomozygous (A/A)heterozygousallele carriers
1000G10578721929
ExAC17500-223315267
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4310.007
-0.040.001
(flanking)-0.0850
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 increased12459wt: 0.8678 / mu: 0.9105 (marginal change - not scored)wt: GCAACCCCAGAGGTC
mu: GCAACCCCAGAGATC
 AACC|ccag
Donor increased12469wt: 0.44 / mu: 0.70wt: AGGTCAGCATGGAGG
mu: AGATCAGCATGGAGG
 GTCA|gcat
Donor increased12462wt: 0.24 / mu: 0.67wt: ACCCCAGAGGTCAGC
mu: ACCCCAGAGATCAGC
 CCCA|gagg
Donor increased12471wt: 0.23 / mu: 0.48wt: GTCAGCATGGAGGAG
mu: ATCAGCATGGAGGAG
 CAGC|atgg
Donor increased12464wt: 0.85 / mu: 0.95wt: CCCAGAGGTCAGCAT
mu: CCCAGAGATCAGCAT
 CAGA|ggtc
distance from splice site 183
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      256AAQKEKDATPEVSMEEDKTVPERS
mutated  all conserved    256AAQKEKDATPEISMEEDKTVPER
Ptroglodytes  all conserved  ENSPTRG00000014616  256AAQKEKDSTPEISVEEDKTVPER
Mmulatta  all conserved  ENSMMUG00000019933  257TAQKEKDSTPEISVEEDKTVPEK
Fcatus  all identical  ENSFCAG00000011241  251PPQKGKESAPEVRAEEEKAVLER
Mmusculus  all identical  ENSMUSG00000056952  267VSQKEESHT-KVSVEKEASALDR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000070618  201AEEEEKHSDLECCSFSEKNNPS-
Dmelanogaster  no homologue    
Celegans  no alignment  Y37H2A.1  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
420420MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
499499METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
501501METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
593593METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
593593METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
630630METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
655655METALDivalent metal cation 2 (By similarity).might get lost (downstream of altered splice site)
707707METALDivalent metal cation 1 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2286 / 2286
position (AA) of stopcodon in wt / mu AA sequence 762 / 762
position of stopcodon in wt / mu cDNA 2448 / 2448
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 163 / 163
chromosome 3
strand 1
last intron/exon boundary 2487
theoretical NMD boundary in CDS 2274
length of CDS 2286
coding sequence (CDS) position 766
cDNA position
(for ins/del: last normal base / first normal base)
928
gDNA position
(for ins/del: last normal base / first normal base)
12466
chromosomal position
(for ins/del: last normal base / first normal base)
10302172
original gDNA sequence snippet AGAAAGACGCAACCCCAGAGGTCAGCATGGAGGAGGATAAG
altered gDNA sequence snippet AGAAAGACGCAACCCCAGAGATCAGCATGGAGGAGGATAAG
original cDNA sequence snippet AGAAAGACGCAACCCCAGAGGTCAGCATGGAGGAGGATAAG
altered cDNA sequence snippet AGAAAGACGCAACCCCAGAGATCAGCATGGAGGAGGATAAG
wildtype AA sequence MASERGKVKH NWSSTSEGCP RKRSCLREPC DVAPSSRPAQ RSASRSGGPS SPKRLKAQKE
DDVACSRRLS WGSSRRRNNS SSSFSPHFLG PGVGGAASKG CLIRNTRGFL SSGGSPLRPA
NASLEEMASL EEEACSLKVD SKDSSHNSTN SEFAAEAEGQ NDTIEEPNKV QKRKRDRLRD
QGSTMIYLKA IQGILGKSMP KRKGEAATRA KPSAAEHPSH GEGPARSEGP AKTAEGAARS
VTVTAAQKEK DATPEVSMEE DKTVPERSSF YDRRVVIDPQ EKPSEEPLGD RRTVIDKCSP
PLEFLDDSDS HLEIQKHKDR EVVMEHPSSG SDWSDVEEIS TVRFSQEEPV SLKPSAVPEP
SSFTTDYVMY PPHLYSSPWC DYASYWTSSP KPSSYPSTGS SSNDAAQVGK SSRSRMSDYS
PNSTGSVQNT SRDMEASEEG WSQNSRSFRF SRSSEEREVK EKRTFQEEMP PRPCGGHASS
SLPKSHLEPS LEEGFIDTHC HLDMLYSKLS FQGTFTKFRK IYSSSFPKEF QGCISDFCDP
RTLTDCLWEE LLKEDLVWGA FGCHPHFARY YSESQERNLL QALRHPKAVA FGEMGLDYSY
KCTTPVPEQH KVFERQLQLA VSLKKPLVIH CREADEDLLE IMKKFVPPDY KIHRHCFTGS
YPVIEPLLKY FPNMSVGFTA VLTYSSAWEA REALRQIPLE RIIVETDAPY FLPRQVPKSL
CQYAHPGLAL HTVREIARVK DQPLSLTLAA LRENTSRLYS L*
mutated AA sequence MASERGKVKH NWSSTSEGCP RKRSCLREPC DVAPSSRPAQ RSASRSGGPS SPKRLKAQKE
DDVACSRRLS WGSSRRRNNS SSSFSPHFLG PGVGGAASKG CLIRNTRGFL SSGGSPLRPA
NASLEEMASL EEEACSLKVD SKDSSHNSTN SEFAAEAEGQ NDTIEEPNKV QKRKRDRLRD
QGSTMIYLKA IQGILGKSMP KRKGEAATRA KPSAAEHPSH GEGPARSEGP AKTAEGAARS
VTVTAAQKEK DATPEISMEE DKTVPERSSF YDRRVVIDPQ EKPSEEPLGD RRTVIDKCSP
PLEFLDDSDS HLEIQKHKDR EVVMEHPSSG SDWSDVEEIS TVRFSQEEPV SLKPSAVPEP
SSFTTDYVMY PPHLYSSPWC DYASYWTSSP KPSSYPSTGS SSNDAAQVGK SSRSRMSDYS
PNSTGSVQNT SRDMEASEEG WSQNSRSFRF SRSSEEREVK EKRTFQEEMP PRPCGGHASS
SLPKSHLEPS LEEGFIDTHC HLDMLYSKLS FQGTFTKFRK IYSSSFPKEF QGCISDFCDP
RTLTDCLWEE LLKEDLVWGA FGCHPHFARY YSESQERNLL QALRHPKAVA FGEMGLDYSY
KCTTPVPEQH KVFERQLQLA VSLKKPLVIH CREADEDLLE IMKKFVPPDY KIHRHCFTGS
YPVIEPLLKY FPNMSVGFTA VLTYSSAWEA REALRQIPLE RIIVETDAPY FLPRQVPKSL
CQYAHPGLAL HTVREIARVK DQPLSLTLAA LRENTSRLYS L*
speed 1.18 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