Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999097681 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM083474)
  • known disease mutation: rs693 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:136405747C>TN/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.440C>T
cDNA.997C>T
g.8462C>T
AA changes P147L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 147
frameshift no
known variant Reference ID: rs113994121
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs693 (pathogenic for Geleophysic dysplasia 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
SP1, Transcription Factor, SP1 Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2081
5.2081
(flanking)-0.9660.441
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 increased8455wt: 0.4314 / mu: 0.4619 (marginal change - not scored)wt: ATGACTATGTCCACATCTCCAGCAAACCGTGTGACCTGCAC
mu: ATGACTATGTCCACATCTCCAGCAAACTGTGTGACCTGCAC		 tcca|GCAA
Donor marginally increased8455wt: 0.9950 / mu: 0.9971 (marginal change - not scored)wt: TCTCCAGCAAACCGT
mu: TCTCCAGCAAACTGT		 TCCA|gcaa
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      147YPDDYVHISSKPCDLHCTTVDGQR
mutated  not conserved    147YPDDYVHISSKLCDLHCTTVDGQ
Ptroglodytes  all identical  ENSPTRG00000022572  256YPDDYVHISSKPCDLHCTTVDGQ
Mmulatta  all identical  ENSMMUG00000017203  147YPDDYVHISSKPCDLHCTTVDGQ
Fcatus  all identical  ENSFCAG00000019127  195YPDDYVHISSKPCDLHCTTVDGQ
Mmusculus  all identical  ENSMUSG00000036040  147YPDDYVHISSKPCDLHCSTVDGQ
Ggallus  all identical  ENSGALG00000002955  158DYVHISSKPCDLHCTTVDGQ
Trubripes  all identical  ENSTRUG00000009723  114YPDDYVHISSNPCDLHCT
Drerio  no alignment  ENSDARG00000074033  n/a
Dmelanogaster  no homologue    
Celegans  no alignment  T19D2.1  n/a
Xtropicalis  no alignment  ENSXETG00000023116  n/a
protein features no protein features affected
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 440
cDNA position
(for ins/del: last normal base / first normal base)		 997
gDNA position
(for ins/del: last normal base / first normal base)		 8462
chromosomal position
(for ins/del: last normal base / first normal base)		 136405747
original gDNA sequence snippet TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA
altered gDNA sequence snippet TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA
original cDNA sequence snippet TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA
altered cDNA sequence snippet TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA
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 SFREEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKLCDL 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 1.03 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