Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997186351263 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM083476)
  • known disease mutation at this position (HGMD CM1618634)
  • known disease mutation: rs694 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:136404921G>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.338G>A
cDNA.553G>A
g.7636G>A
AA changes R113H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs113994122
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs694 (pathogenic for Geleophysic dysplasia 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1618634)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1618634)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083476)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1618634)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083476)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083476)
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)1.7631
5.6421
(flanking)-3.9730.003
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: 0.9616 (marginal change - not scored)wt: CGCGAGGAGCAGTGC
mu: CACGAGGAGCAGTGC		 CGAG|gagc
Donor marginally increased7637wt: 0.9893 / mu: 0.9906 (marginal change - not scored)wt: TTCCGCGAGGAGCAG
mu: TTCCACGAGGAGCAG		 CCGC|gagg
Donor increased7634wt: 0.36 / mu: 0.45wt: AGCTTCCGCGAGGAG
mu: AGCTTCCACGAGGAG		 CTTC|cgcg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113VQECPPDGRSFREEQCVSFNSHVY
mutated  not conserved    113VQECPPDGRSFHEEQCVSF
Ptroglodytes  all identical  ENSPTRG00000022572  222VQECPPDGRSFREEQCVSF
Mmulatta  all identical  ENSMMUG00000017203  113VQECPPDGRSFREEQCVSF
Fcatus  all identical  ENSFCAG00000019127  161LQECPPDGRSFREEQCISF
Mmusculus  all identical  ENSMUSG00000036040  113VQECPPDGRSFREEQCVSF
Ggallus  all identical  ENSGALG00000002955  124VQECPANGRSFREEQCSSFNSHV
Trubripes  all identical  ENSTRUG00000009723  80SKECPATGRSFREEQCWSFNSQL
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 338
cDNA position
(for ins/del: last normal base / first normal base)		 553
gDNA position
(for ins/del: last normal base / first normal base)		 7636
chromosomal position
(for ins/del: last normal base / first normal base)		 136404921
original gDNA sequence snippet GCCGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCT
altered gDNA sequence snippet GCCGGACGGGAGGAGCTTCCACGAGGAGCAGTGCGTCTCCT
original cDNA sequence snippet GCCGGACGGGAGGAGCTTCCGCGAGGAGCAGTGCGTCTCCT
altered cDNA sequence snippet GCCGGACGGGAGGAGCTTCCACGAGGAGCAGTGCGTCTCCT
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 SFHEEQCVSF
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 0.97 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