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: ENST00000378387
Querying Taster for transcript #2: ENST00000378395
Querying Taster for transcript #3: ENST00000343259
MT speed 4.27 s - this script 7.055548 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARHGEF39polymorphism_automatic0.00061902153307003simple_aaeaffectedH306Rsingle base exchangers2297879show file
ARHGEF39polymorphism_automatic0.00061902153307003simple_aaeaffectedH270Rsingle base exchangers2297879show file
ARHGEF39polymorphism_automatic0.304967622730557without_aaeaffectedsingle base exchangers2297879show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99938097846693 (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) chr9:35662251T>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF39
Ensembl transcript ID ENST00000378387
Genbank transcript ID NM_032818
UniProt peptide Q8N4T4
alteration type single base exchange
alteration region CDS
DNA changes c.917A>G
cDNA.1035A>G
g.13613A>G
AA changes H306R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
306
frameshift no
known variant Reference ID: rs2297879
databasehomozygous (C/C)heterozygousallele carriers
1000G3019291230
ExAC67631924126004
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.3930.036
0.6690.408
(flanking)0.5410.64
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased13612wt: 0.78 / mu: 0.93wt: CTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATG
mu: CTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATG
 cctc|ATGA
Acc marginally increased13609wt: 0.8486 / mu: 0.9262 (marginal change - not scored)wt: TCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTT
mu: TCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTT
 ttcc|CTCA
Acc increased13607wt: 0.43 / mu: 0.52wt: GGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGC
mu: GGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGC
 cctt|CCCT
Acc marginally increased13614wt: 0.9612 / mu: 0.9644 (marginal change - not scored)wt: CTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTC
mu: CTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTC
 tcat|GAGA
Acc increased13605wt: 0.60 / mu: 0.76wt: GTGGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACT
mu: GTGGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACT
 gtcc|TTCC
Acc increased13618wt: 0.21 / mu: 0.26wt: AGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTCCACA
mu: AGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTCCACA
 gaga|AGCT
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      306PCGGLLSLSFPHEKLLLMSTDQEE
mutated  not conserved    306SLSFPREKLLLMSTDQE
Ptroglodytes  all identical  ENSPTRG00000020915  306SLSFPHEKLLLMSTDQE
Mmulatta  all identical  ENSMMUG00000016323  306SLSFPHEKLLLMSTDQE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000051517  306SLSFPHEKLLLMSTDQE
Ggallus  all identical  ENSGALG00000002599  314E-GGLLSLSFPHKT
Trubripes  not conserved  ENSTRUG00000012270  312NFPKAKLLLMSSSQE
Drerio  not conserved  ENSDARG00000013476  310ARAKLLLMSDDQV
Dmelanogaster  no alignment  FBgn0035761  n/a
Celegans  no alignment  C02F12.4  n/a
Xtropicalis  not conserved  ENSXETG00000020139  319R-GGLISLTFAKEKLLLMSTDQK
protein features
start (aa)end (aa)featuredetails 
227331DOMAINPH.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1008 / 1008
position (AA) of stopcodon in wt / mu AA sequence 336 / 336
position of stopcodon in wt / mu cDNA 1126 / 1126
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 119 / 119
chromosome 9
strand -1
last intron/exon boundary 1111
theoretical NMD boundary in CDS 942
length of CDS 1008
coding sequence (CDS) position 917
cDNA position
(for ins/del: last normal base / first normal base)
1035
gDNA position
(for ins/del: last normal base / first normal base)
13613
chromosomal position
(for ins/del: last normal base / first normal base)
35662251
original gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
original cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
wildtype AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TRAARLISET AQRVHTIGQK QKNDQHLRRV QALLSGRQAK GLTSGRWFLR QGWLLVVPPH
GEPRPRMFFL FTDVLLMAKP RPPLHLLRSG TFACKALYPM AQCHLSRVFG HSGGPCGGLL
SLSFPHEKLL LMSTDQEELS RWYHSLTWAI SSQKN*
mutated AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TRAARLISET AQRVHTIGQK QKNDQHLRRV QALLSGRQAK GLTSGRWFLR QGWLLVVPPH
GEPRPRMFFL FTDVLLMAKP RPPLHLLRSG TFACKALYPM AQCHLSRVFG HSGGPCGGLL
SLSFPREKLL LMSTDQEELS RWYHSLTWAI SSQKN*
speed 1.49 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: 0.99938097846693 (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) chr9:35662251T>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF39
Ensembl transcript ID ENST00000378395
Genbank transcript ID N/A
UniProt peptide Q8N4T4
alteration type single base exchange
alteration region CDS
DNA changes c.809A>G
cDNA.809A>G
g.13613A>G
AA changes H270R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
270
frameshift no
known variant Reference ID: rs2297879
databasehomozygous (C/C)heterozygousallele carriers
1000G3019291230
ExAC67631924126004
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.3930.036
0.6690.408
(flanking)0.5410.64
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased13612wt: 0.78 / mu: 0.93wt: CTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATG
mu: CTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATG
 cctc|ATGA
Acc marginally increased13609wt: 0.8486 / mu: 0.9262 (marginal change - not scored)wt: TCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTT
mu: TCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTT
 ttcc|CTCA
Acc increased13607wt: 0.43 / mu: 0.52wt: GGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGC
mu: GGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGC
 cctt|CCCT
Acc marginally increased13614wt: 0.9612 / mu: 0.9644 (marginal change - not scored)wt: CTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTC
mu: CTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTC
 tcat|GAGA
Acc increased13605wt: 0.60 / mu: 0.76wt: GTGGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACT
mu: GTGGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACT
 gtcc|TTCC
Acc increased13618wt: 0.21 / mu: 0.26wt: AGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTCCACA
mu: AGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTCCACA
 gaga|AGCT
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      270PCGGLLSLSFPHEKLLLMSTDQEE
mutated  not conserved    270PCGGLLSLSFPREKLLLMSTDQE
Ptroglodytes  all identical  ENSPTRG00000020915  306PCGGLLSLSFPHEKLLLMSTDQE
Mmulatta  all identical  ENSMMUG00000016323  306PCGGLLSLSFPHEKLLLMSTDQE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000051517  306PCGGLLSLSFPHEKLLLMSTDQE
Ggallus  all identical  ENSGALG00000002599  314E-GGLLSLSFPHKTLLLMSTDQQ
Trubripes  not conserved  ENSTRUG00000012270  313Q-GGLLSLNFPKAKLLLMSSSQE
Drerio  not conserved  ENSDARG00000013476  311Q-GGLISLTFARAKLLLMSDDQV
Dmelanogaster  no alignment  FBgn0035761  n/a
Celegans  no alignment  C02F12.4  n/a
Xtropicalis  not conserved  ENSXETG00000020139  319R-GGLISLTFAKEKLLLMST
protein features
start (aa)end (aa)featuredetails 
227331DOMAINPH.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 900 / 900
position (AA) of stopcodon in wt / mu AA sequence 300 / 300
position of stopcodon in wt / mu cDNA 900 / 900
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 1 / 1
chromosome 9
strand -1
last intron/exon boundary 885
theoretical NMD boundary in CDS 834
length of CDS 900
coding sequence (CDS) position 809
cDNA position
(for ins/del: last normal base / first normal base)
809
gDNA position
(for ins/del: last normal base / first normal base)
13613
chromosomal position
(for ins/del: last normal base / first normal base)
35662251
original gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
original cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
wildtype AA sequence MLGVCQTLKQ YFLGILKAKG TLRPPERQAL FGSWELIYGA SQELLPYLEG GCWGQGLEGF
CRHLELYNQF AANSERSQTT LQEQLKKNKG FRRFVRLQEG RPEFGGLQLQ DLLPLPLQRL
QQYENLVVAL AENTGPNSPD HQQLTRAARL ISETAQRVHT IGQKQKNDQH LRRVQALLSG
RQAKGLTSGR WFLRQGWLLV VPPHGEPRPR MFFLFTDVLL MAKPRPPLHL LRSGTFACKA
LYPMAQCHLS RVFGHSGGPC GGLLSLSFPH EKLLLMSTDQ EELSRWYHSL TWAISSQKN*
mutated AA sequence MLGVCQTLKQ YFLGILKAKG TLRPPERQAL FGSWELIYGA SQELLPYLEG GCWGQGLEGF
CRHLELYNQF AANSERSQTT LQEQLKKNKG FRRFVRLQEG RPEFGGLQLQ DLLPLPLQRL
QQYENLVVAL AENTGPNSPD HQQLTRAARL ISETAQRVHT IGQKQKNDQH LRRVQALLSG
RQAKGLTSGR WFLRQGWLLV VPPHGEPRPR MFFLFTDVLL MAKPRPPLHL LRSGTFACKA
LYPMAQCHLS RVFGHSGGPC GGLLSLSFPR EKLLLMSTDQ EELSRWYHSL TWAISSQKN*
speed 1.49 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: 0.695032377269443 (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) chr9:35662251T>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF39
Ensembl transcript ID ENST00000343259
Genbank transcript ID N/A
UniProt peptide Q8N4T4
alteration type single base exchange
alteration region CDS
DNA changes c.558A>G
cDNA.670A>G
g.13613A>G
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift no
known variant Reference ID: rs2297879
databasehomozygous (C/C)heterozygousallele carriers
1000G3019291230
ExAC67631924126004
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.3930.036
0.6690.408
(flanking)0.5410.64
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 188)
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased13612wt: 0.78 / mu: 0.93wt: CTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATG
mu: CTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATG
 cctc|ATGA
Acc marginally increased13609wt: 0.8486 / mu: 0.9262 (marginal change - not scored)wt: TCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTT
mu: TCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTT
 ttcc|CTCA
Acc increased13607wt: 0.43 / mu: 0.52wt: GGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGC
mu: GGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGC
 cctt|CCCT
Acc marginally increased13614wt: 0.9612 / mu: 0.9644 (marginal change - not scored)wt: CTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTC
mu: CTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTC
 tcat|GAGA
Acc increased13605wt: 0.60 / mu: 0.76wt: GTGGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACT
mu: GTGGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACT
 gtcc|TTCC
Acc increased13618wt: 0.21 / mu: 0.26wt: AGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTCCACA
mu: AGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTCCACA
 gaga|AGCT
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
22197DOMAINDH.might get lost (downstream of altered splice site)
227331DOMAINPH.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 673 / 673
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 113 / 113
chromosome 9
strand -1
last intron/exon boundary 746
theoretical NMD boundary in CDS 583
length of CDS 561
coding sequence (CDS) position 558
cDNA position
(for ins/del: last normal base / first normal base)
670
gDNA position
(for ins/del: last normal base / first normal base)
13613
chromosomal position
(for ins/del: last normal base / first normal base)
35662251
original gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
original cDNA sequence snippet CTCACACCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered cDNA sequence snippet CTCACACCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
wildtype AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TPVLPS*
mutated AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TPVLPS*
speed 1.29 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