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: ENST00000354484
Querying Taster for transcript #2: ENST00000393061
Querying Taster for transcript #3: ENST00000393060
MT speed 0 s - this script 4.532073 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADAMTSL2disease_causing0.999999788498679simple_aaeaffectedE223Ksingle base exchangers113994123show file
ADAMTSL2disease_causing0.999999788498679simple_aaeaffectedE114Ksingle base exchangers113994123show file
ADAMTSL2disease_causing0.999999788498679simple_aaeaffectedE114Ksingle base exchangers113994123show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999788498679      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs695 (probable pathogenic)
  • known disease mutation at this position (HGMD CM083475)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:136404923G>AN/A show variant in all transcripts   IGV
HGNC symbol ADAMTSL2
Ensembl transcript ID ENST00000393061
Genbank transcript ID NM_014694
UniProt peptide Q86TH1
alteration type single base exchange
alteration region CDS
DNA changes c.667G>A
cDNA.1099G>A
g.7638G>A
AA changes E223K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
223
frameshift no
known variant Reference ID: rs113994123
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs695 (probable pathogenic for Geleophysic dysplasia 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.9730.003
5.6421
(flanking)4.6721
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 increased7640wt: 0.9266 / mu: 0.9669 (marginal change - not scored)wt: CGCGAGGAGCAGTGC
mu: CGCAAGGAGCAGTGC
 CGAG|gagc
Donor increased7634wt: 0.36 / mu: 0.76wt: AGCTTCCGCGAGGAG
mu: AGCTTCCGCAAGGAG
 CTTC|cgcg
Donor marginally increased7635wt: 0.9780 / mu: 0.9833 (marginal change - not scored)wt: GCTTCCGCGAGGAGC
mu: GCTTCCGCAAGGAGC
 TTCC|gcga
Donor increased7642wt: 0.69 / mu: 0.87wt: CGAGGAGCAGTGCGT
mu: CAAGGAGCAGTGCGT
 AGGA|gcag
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      223QECPPDGRSFREEQCVSFNSHVYN
mutated  all conserved    223QECPPDGRSFRKEQCVSFNSHVY
Ptroglodytes  all identical  ENSPTRG00000022572  223QECPPDGRSFREEQCVSFNSHVY
Mmulatta  all identical  ENSMMUG00000017203  114QECPPDGRSFREEQCVSF
Fcatus  all identical  ENSFCAG00000019127  162QECPPDGRSFREEQCISFNSRVY
Mmusculus  all identical  ENSMUSG00000036040  114QECPPDGRSFREEQCVSF
Ggallus  all identical  ENSGALG00000002955  125QECPANGRSFREEQCSSFNSHVY
Trubripes  all identical  ENSTRUG00000009723  81KECPATGRSFREEQCWSFNSQLY
Drerio  no alignment  ENSDARG00000074033  n/a
Dmelanogaster  no homologue    
Celegans  no alignment  T19D2.1  n/a
Xtropicalis  no alignment  ENSXETG00000023116  n/a
protein features
start (aa)end (aa)featuredetails 
367367CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
428428CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
475475CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
511511CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
524524CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
533533CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
544544CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
564618DOMAINTSP type-1 2.might get lost (downstream of altered splice site)
622686DOMAINTSP type-1 3.might get lost (downstream of altered splice site)
688736DOMAINTSP type-1 4.might get lost (downstream of altered splice site)
731731CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
737795DOMAINTSP type-1 5.might get lost (downstream of altered splice site)
797851DOMAINTSP type-1 6.might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
853908DOMAINTSP type-1 7.might get lost (downstream of altered splice site)
912950DOMAINPLAC.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3183 / 3183
position (AA) of stopcodon in wt / mu AA sequence 1061 / 1061
position of stopcodon in wt / mu cDNA 3615 / 3615
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 433 / 433
chromosome 9
strand 1
last intron/exon boundary 3497
theoretical NMD boundary in CDS 3014
length of CDS 3183
coding sequence (CDS) position 667
cDNA position
(for ins/del: last normal base / first normal base)
1099
gDNA position
(for ins/del: last normal base / first normal base)
7638
chromosomal position
(for ins/del: last normal base / first normal base)
136404923
original gDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered gDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
original cDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered cDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
wildtype AA sequence MLFEVGEGGG AGEEGKGRGR PGRSLCTHAA PARTAHLAPS ALRSARPFLW EDNLLTRSQG
LPDNHDQLVP DNLEAWALAG PRGLFPKRTL VIWKRIGAGL VVTVALLPRM DGRWQCSCWA
WFLLVLAVVA GDTVSTGSTD NSPTSNSLEG GTDATAFWWG EWTKWTACSR SCGGGVTSQE
RHCLQQRRKS VPGPGNRTCT GTSKRYQLCR VQECPPDGRS FREEQCVSFN SHVYNGRTHQ
WKPLYPDDYV HISSKPCDLH CTTVDGQRQL MVPARDGTSC KLTDLRGVCV SGKCEPIGCD
GVLFSTHTLD KCGICQGDGS SCTHVTGNYR KGNAHLGYSL VTHIPAGARD IQIVERKKSA
DVLALADEAG YYFFNGNYKV DSPKNFNIAG TVVKYRRPMD VYETGIEYIV AQGPTNQGLN
VMVWNQNGKS PSITFEYTLL QPPHESRPQP IYYGFSESAE SQGLDGAGLM GFVPHNGSLY
GQASSERLGL DNRLFGHPGL DMELGPSQGQ ETNEVCEQAG GGACEGPPRG KGFRDRNVTG
TPLTGDKDDE EVDTHFASQE FFSANAISDQ LLGAGSDLKD FTLNETVNSI FAQGAPRSSL
AESFFVDYEE NEGAGPYLLN GSYLELSSDR VANSSSEAPF PNVSTSLLTS AGNRTHKART
RPKARKQGVS PADMYRWKLS SHEPCSATCT TGVMSAYAMC VRYDGVEVDD SYCDALTRPE
PVHEFCAGRE CQPRWETSSW SECSRTCGEG YQFRVVRCWK MLSPGFDSSV YSDLCEAAEA
VRPEERKTCR NPACGPQWEM SEWSECTAKC GERSVVTRDI RCSEDEKLCD PNTRPVGEKN
CTGPPCDRQW TVSDWGPCSG SCGQGRTIRH VYCKTSDGRV VPESQCQMET KPLAIHPCGD
KNCPAHWLAQ DWERCNTTCG RGVKKRLVLC MELANGKPQT RSGPECGLAK KPPEESTCFE
RPCFKWYTSP WSECTKTCGV GVRMRDVKCY QGTDIVRGCD PLVKPVGRQA CDLQPCPTEP
PDDSCQDQPG TNCALAIKVN LCGHWYYSKA CCRSCRPPHS *
mutated AA sequence MLFEVGEGGG AGEEGKGRGR PGRSLCTHAA PARTAHLAPS ALRSARPFLW EDNLLTRSQG
LPDNHDQLVP DNLEAWALAG PRGLFPKRTL VIWKRIGAGL VVTVALLPRM DGRWQCSCWA
WFLLVLAVVA GDTVSTGSTD NSPTSNSLEG GTDATAFWWG EWTKWTACSR SCGGGVTSQE
RHCLQQRRKS VPGPGNRTCT GTSKRYQLCR VQECPPDGRS FRKEQCVSFN SHVYNGRTHQ
WKPLYPDDYV HISSKPCDLH CTTVDGQRQL MVPARDGTSC KLTDLRGVCV SGKCEPIGCD
GVLFSTHTLD KCGICQGDGS SCTHVTGNYR KGNAHLGYSL VTHIPAGARD IQIVERKKSA
DVLALADEAG YYFFNGNYKV DSPKNFNIAG TVVKYRRPMD VYETGIEYIV AQGPTNQGLN
VMVWNQNGKS PSITFEYTLL QPPHESRPQP IYYGFSESAE SQGLDGAGLM GFVPHNGSLY
GQASSERLGL DNRLFGHPGL DMELGPSQGQ ETNEVCEQAG GGACEGPPRG KGFRDRNVTG
TPLTGDKDDE EVDTHFASQE FFSANAISDQ LLGAGSDLKD FTLNETVNSI FAQGAPRSSL
AESFFVDYEE NEGAGPYLLN GSYLELSSDR VANSSSEAPF PNVSTSLLTS AGNRTHKART
RPKARKQGVS PADMYRWKLS SHEPCSATCT TGVMSAYAMC VRYDGVEVDD SYCDALTRPE
PVHEFCAGRE CQPRWETSSW SECSRTCGEG YQFRVVRCWK MLSPGFDSSV YSDLCEAAEA
VRPEERKTCR NPACGPQWEM SEWSECTAKC GERSVVTRDI RCSEDEKLCD PNTRPVGEKN
CTGPPCDRQW TVSDWGPCSG SCGQGRTIRH VYCKTSDGRV VPESQCQMET KPLAIHPCGD
KNCPAHWLAQ DWERCNTTCG RGVKKRLVLC MELANGKPQT RSGPECGLAK KPPEESTCFE
RPCFKWYTSP WSECTKTCGV GVRMRDVKCY QGTDIVRGCD PLVKPVGRQA CDLQPCPTEP
PDDSCQDQPG TNCALAIKVN LCGHWYYSKA CCRSCRPPHS *
speed 1.10 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: 0.999999788498679      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs695 (probable pathogenic)
  • known disease mutation at this position (HGMD CM083475)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:136404923G>AN/A show variant in all transcripts   IGV
HGNC symbol ADAMTSL2
Ensembl transcript ID ENST00000354484
Genbank transcript ID NM_001145320
UniProt peptide Q86TH1
alteration type single base exchange
alteration region CDS
DNA changes c.340G>A
cDNA.897G>A
g.7638G>A
AA changes E114K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
114
frameshift no
known variant Reference ID: rs113994123
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs695 (probable pathogenic for Geleophysic dysplasia 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.9730.003
5.6421
(flanking)4.6721
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 increased7640wt: 0.9266 / mu: 0.9669 (marginal change - not scored)wt: CGCGAGGAGCAGTGC
mu: CGCAAGGAGCAGTGC
 CGAG|gagc
Donor increased7634wt: 0.36 / mu: 0.76wt: AGCTTCCGCGAGGAG
mu: AGCTTCCGCAAGGAG
 CTTC|cgcg
Donor marginally increased7635wt: 0.9780 / mu: 0.9833 (marginal change - not scored)wt: GCTTCCGCGAGGAGC
mu: GCTTCCGCAAGGAGC
 TTCC|gcga
Donor increased7642wt: 0.69 / mu: 0.87wt: CGAGGAGCAGTGCGT
mu: CAAGGAGCAGTGCGT
 AGGA|gcag
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      114QECPPDGRSFREEQCVSFNSHVYN
mutated  all conserved    114QECPPDGRSFRKEQCVSF
Ptroglodytes  all identical  ENSPTRG00000022572  223QECPPDGRSFREEQCVSF
Mmulatta  all identical  ENSMMUG00000017203  114QECPPDGRSFREEQCVSF
Fcatus  all identical  ENSFCAG00000019127  162QECPPDGRSFREEQCISF
Mmusculus  all identical  ENSMUSG00000036040  114QECPPDGRSFREEQCVSF
Ggallus  all identical  ENSGALG00000002955  125QECPANGRSFREEQCSSFNSHVY
Trubripes  all identical  ENSTRUG00000009723  81KECPATGRSFREEQCWSFNSQLY
Drerio  no alignment  ENSDARG00000074033  n/a
Dmelanogaster  no homologue    
Celegans  no alignment  T19D2.1  n/a
Xtropicalis  no alignment  ENSXETG00000023116  n/a
protein features
start (aa)end (aa)featuredetails 
367367CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
428428CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
475475CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
511511CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
524524CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
533533CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
544544CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
564618DOMAINTSP type-1 2.might get lost (downstream of altered splice site)
622686DOMAINTSP type-1 3.might get lost (downstream of altered splice site)
688736DOMAINTSP type-1 4.might get lost (downstream of altered splice site)
731731CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
737795DOMAINTSP type-1 5.might get lost (downstream of altered splice site)
797851DOMAINTSP type-1 6.might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
853908DOMAINTSP type-1 7.might get lost (downstream of altered splice site)
912950DOMAINPLAC.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2856 / 2856
position (AA) of stopcodon in wt / mu AA sequence 952 / 952
position of stopcodon in wt / mu cDNA 3413 / 3413
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 558 / 558
chromosome 9
strand 1
last intron/exon boundary 3295
theoretical NMD boundary in CDS 2687
length of CDS 2856
coding sequence (CDS) position 340
cDNA position
(for ins/del: last normal base / first normal base)
897
gDNA position
(for ins/del: last normal base / first normal base)
7638
chromosomal position
(for ins/del: last normal base / first normal base)
136404923
original gDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered gDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
original cDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered cDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
wildtype AA sequence MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFREEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKPCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*
mutated AA sequence MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFRKEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKPCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*
speed 1.02 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: 0.999999788498679      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs695 (probable pathogenic)
  • known disease mutation at this position (HGMD CM083475)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:136404923G>AN/A show variant in all transcripts   IGV
HGNC symbol ADAMTSL2
Ensembl transcript ID ENST00000393060
Genbank transcript ID N/A
UniProt peptide Q86TH1
alteration type single base exchange
alteration region CDS
DNA changes c.340G>A
cDNA.555G>A
g.7638G>A
AA changes E114K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
114
frameshift no
known variant Reference ID: rs113994123
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs695 (probable pathogenic for Geleophysic dysplasia 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083475)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.9730.003
5.6421
(flanking)4.6721
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 increased7640wt: 0.9266 / mu: 0.9669 (marginal change - not scored)wt: CGCGAGGAGCAGTGC
mu: CGCAAGGAGCAGTGC
 CGAG|gagc
Donor increased7634wt: 0.36 / mu: 0.76wt: AGCTTCCGCGAGGAG
mu: AGCTTCCGCAAGGAG
 CTTC|cgcg
Donor marginally increased7635wt: 0.9780 / mu: 0.9833 (marginal change - not scored)wt: GCTTCCGCGAGGAGC
mu: GCTTCCGCAAGGAGC
 TTCC|gcga
Donor increased7642wt: 0.69 / mu: 0.87wt: CGAGGAGCAGTGCGT
mu: CAAGGAGCAGTGCGT
 AGGA|gcag
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      114QECPPDGRSFREEQCVSFNSHVYN
mutated  all conserved    114QECPPDGRSFRKEQCVSF
Ptroglodytes  all identical  ENSPTRG00000022572  223QECPPDGRSFREEQCVSF
Mmulatta  all identical  ENSMMUG00000017203  114QECPPDGRSFREEQCVSF
Fcatus  all identical  ENSFCAG00000019127  162QECPPDGRSFREEQCISF
Mmusculus  all identical  ENSMUSG00000036040  114QECPPDGRSFREEQCVSF
Ggallus  all identical  ENSGALG00000002955  125QECPANGRSFREEQCSSFNSHVY
Trubripes  all identical  ENSTRUG00000009723  81KECPATGRSFREEQCWSFNSQLY
Drerio  no alignment  ENSDARG00000074033  n/a
Dmelanogaster  no homologue    
Celegans  no alignment  T19D2.1  n/a
Xtropicalis  no alignment  ENSXETG00000023116  n/a
protein features
start (aa)end (aa)featuredetails 
367367CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
428428CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
475475CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
511511CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
524524CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
533533CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
544544CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
564618DOMAINTSP type-1 2.might get lost (downstream of altered splice site)
622686DOMAINTSP type-1 3.might get lost (downstream of altered splice site)
688736DOMAINTSP type-1 4.might get lost (downstream of altered splice site)
731731CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
737795DOMAINTSP type-1 5.might get lost (downstream of altered splice site)
797851DOMAINTSP type-1 6.might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
853908DOMAINTSP type-1 7.might get lost (downstream of altered splice site)
912950DOMAINPLAC.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2856 / 2856
position (AA) of stopcodon in wt / mu AA sequence 952 / 952
position of stopcodon in wt / mu cDNA 3071 / 3071
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 216 / 216
chromosome 9
strand 1
last intron/exon boundary 2953
theoretical NMD boundary in CDS 2687
length of CDS 2856
coding sequence (CDS) position 340
cDNA position
(for ins/del: last normal base / first normal base)
555
gDNA position
(for ins/del: last normal base / first normal base)
7638
chromosomal position
(for ins/del: last normal base / first normal base)
136404923
original gDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered gDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
original cDNA sequence snippet CGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCTTC
altered cDNA sequence snippet CGGACGGGAGGAGCTTCCGCAAGGAGCAGTGCGTCTCCTTC
wildtype AA sequence MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFREEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKPCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*
mutated AA sequence MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFRKEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKPCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*
speed 1.15 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