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 7 transcript(s)...
Querying Taster for transcript #1: ENST00000374840
Querying Taster for transcript #2: ENST00000374832
Querying Taster for transcript #3: ENST00000374830
Querying Taster for transcript #4: ENST00000374829
Querying Taster for transcript #5: ENST00000425315
Querying Taster for transcript #6: ENST00000539907
Querying Taster for transcript #7: ENST00000540617
MT speed 0 s - this script 5.058924 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALPLdisease_causing_automatic0.999999776718175simple_aaeaffected0G334Dsingle base exchangers121918009show file
ALPLdisease_causing_automatic0.999999776718175simple_aaeaffected0G334Dsingle base exchangers121918009show file
ALPLdisease_causing_automatic0.999999776718175simple_aaeaffected0G334Dsingle base exchangers121918009show file
ALPLdisease_causing_automatic0.999999776718175simple_aaeaffected0G257Dsingle base exchangers121918009show file
ALPLdisease_causing_automatic0.999999776718175simple_aaeaffected0G279Dsingle base exchangers121918009show file
ALPLdisease_causing_automatic1without_aaeaffected0single base exchangers121918009show file
ALPLdisease_causing_automatic1without_aaeaffected0single base exchangers121918009show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999776718175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374840
Genbank transcript ID NM_000478
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.1001G>A
cDNA.1251G>A
g.66372G>A
AA changes G334D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 334
frameshift no
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
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 increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      334NPKGFFLLVEGGRIDHGHHEGKAK
mutated  not conserved    334NPKGFFLLVEGDRIDHGHHEGKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  334NPKGFFLLVEGGRIDHGHHEGKA
Fcatus  all identical  ENSFCAG00000002960  334NPKGFFLLVEGGRIDHGHHEGKA
Mmusculus  all identical  ENSMUSG00000028766  334NLKGFFLLVEGGRIDHGHHEGKA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  334NPNGFYLLVEGGRIDHGHHEGKA
Drerio  all identical  ENSDARG00000015546  370NERGFFLLVEGGRIDHGHHEGKA
Dmelanogaster  all identical  FBgn0043791  366QSAGRGYFLFVEGGRIDHGHHDTLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1825 / 1825
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 251 / 251
chromosome 1
strand 1
last intron/exon boundary 1560
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 1001
cDNA position
(for ins/del: last normal base / first normal base)		 1251
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
mutated AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGDRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 0.92 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: 0.999999776718175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374832
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.1001G>A
cDNA.1255G>A
g.66372G>A
AA changes G334D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 334
frameshift no
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
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 increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      334NPKGFFLLVEGGRIDHGHHEGKAK
mutated  not conserved    334NPKGFFLLVEGDRIDHGHHEGKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  334NPKGFFLLVEGGRIDHGHHEGKA
Fcatus  all identical  ENSFCAG00000002960  334NPKGFFLLVEGGRIDHGHHEGKA
Mmusculus  all identical  ENSMUSG00000028766  334NLKGFFLLVEGGRIDHGHHEGKA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  334NPNGFYLLVEGGRIDHGHHEGKA
Drerio  all identical  ENSDARG00000015546  370NERGFFLLVEGGRIDHGHHEGKA
Dmelanogaster  all identical  FBgn0043791  366QSAGRGYFLFVEGGRIDHGHHDTLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1829 / 1829
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 255 / 255
chromosome 1
strand 1
last intron/exon boundary 1564
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 1001
cDNA position
(for ins/del: last normal base / first normal base)		 1255
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
mutated AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGDRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 0.95 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: 0.999999776718175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000425315
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.1001G>A
cDNA.1001G>A
g.66372G>A
AA changes G334D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 334
frameshift no
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
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 increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      334NPKGFFLLVEGGRIDHGHHEGKAK
mutated  not conserved    334NPKGFFLLVEGDRIDHGHHEGKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  334NPKGFFLLVEGGRIDHGHHEGKA
Fcatus  all identical  ENSFCAG00000002960  334NPKGFFLLVEGGRIDHGHHEGKA
Mmusculus  all identical  ENSMUSG00000028766  334NLKGFFLLVEGGRIDHGHHEGKA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  334NPNGFYLLVEGGRIDHGHHEGKA
Drerio  all identical  ENSDARG00000015546  370NERGFFLLVEGGRIDHGHHEGKA
Dmelanogaster  all identical  FBgn0043791  366QSAGRGYFLFVEGGRIDHGHHDTLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1575 / 1575
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 1
strand 1
last intron/exon boundary 1310
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 1001
cDNA position
(for ins/del: last normal base / first normal base)		 1001
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
mutated AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGDRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 0.59 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: 0.999999776718175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000539907
Genbank transcript ID NM_001177520
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.770G>A
cDNA.977G>A
g.66372G>A
AA changes G257D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
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 increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257NPKGFFLLVEGGRIDHGHHEGKAK
mutated  not conserved    257NPKGFFLLVEGDRIDHGHHEGKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  334NPKGFFLLVEGGRIDHG
Fcatus  all identical  ENSFCAG00000002960  334NPKGFFLLVEGGRIDHG
Mmusculus  all identical  ENSMUSG00000028766  334NLKGFFLLVEGGRIDHG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  334NPNGFYLLVEGGRIDHGHHEGKA
Drerio  all identical  ENSDARG00000015546  370NERGFFLLVEGGRIDHG
Dmelanogaster  all identical  FBgn0043791  368GGRIDHGHHDTLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1344 / 1344
position (AA) of stopcodon in wt / mu AA sequence 448 / 448
position of stopcodon in wt / mu cDNA 1551 / 1551
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 208 / 208
chromosome 1
strand 1
last intron/exon boundary 1286
theoretical NMD boundary in CDS 1028
length of CDS 1344
coding sequence (CDS) position 770
cDNA position
(for ins/del: last normal base / first normal base)		 977
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
mutated AA sequence MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGDRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
speed 0.88 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: 0.999999776718175 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000540617
Genbank transcript ID NM_001127501
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.836G>A
cDNA.1093G>A
g.66372G>A
AA changes G279D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 279
frameshift no
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
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 increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      279NPKGFFLLVEGGRIDHGHHEGKAK
mutated  not conserved    279NPKGFFLLVEGDRIDHGHHEGKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  334NPKGFFLLVEGGRIDHGHHEGKA
Fcatus  all identical  ENSFCAG00000002960  334NPKGFFLLVEGGRIDHGHHEGKA
Mmusculus  all identical  ENSMUSG00000028766  334NLKGFFLLVEGGRIDHGHHEGKA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  334NPNGFYLLVEGGRIDHGHHEGKA
Drerio  all identical  ENSDARG00000015546  370NERGFFLLVEGGRIDHGHHEGKA
Dmelanogaster  all identical  FBgn0043791  366QSAGRGYFLFVEGGRIDHGHHDTLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1410 / 1410
position (AA) of stopcodon in wt / mu AA sequence 470 / 470
position of stopcodon in wt / mu cDNA 1667 / 1667
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 258 / 258
chromosome 1
strand 1
last intron/exon boundary 1402
theoretical NMD boundary in CDS 1094
length of CDS 1410
coding sequence (CDS) position 836
cDNA position
(for ins/del: last normal base / first normal base)		 1093
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet CTTCTTGCTGGTGGAAGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MFLGDGMGVS TVTAARILKG QLHHNPGEET RLEMDKFPFV ALSKTYNTNA QVPDSAGTAT
AYLCGVKANE GTVGVSAATE RSRCNTTQGN EVTSILRWAK DAGKSVGIVT TTRVNHATPS
AAYAHSADRD WYSDNEMPPE ALSQGCKDIA YQLMHNIRDI DVIMGGGRKY MYPKNKTDVE
YESDEKARGT RLDGLDLVDT WKSFKPRYKH SHFIWNRTEL LTLDPHNVDY LLGLFEPGDM
QYELNRNNVT DPSLSEMVVV AIQILRKNPK GFFLLVEGGR IDHGHHEGKA KQALHEAVEM
DRAIGQAGSL TSSEDTLTVV TADHSHVFTF GGYTPRGNSI FGLAPMLSDT DKKPFTAILY
GNGPGYKVVG GERENVSMVD YAHNNYQAQS AVPLRHETHG GEDVAVFSKG PMAHLLHGVH
EQNYVPHVMA YAACIGANLG HCAPASSAGS LAAGPLLLAL ALYPLSVLF*
mutated AA sequence MFLGDGMGVS TVTAARILKG QLHHNPGEET RLEMDKFPFV ALSKTYNTNA QVPDSAGTAT
AYLCGVKANE GTVGVSAATE RSRCNTTQGN EVTSILRWAK DAGKSVGIVT TTRVNHATPS
AAYAHSADRD WYSDNEMPPE ALSQGCKDIA YQLMHNIRDI DVIMGGGRKY MYPKNKTDVE
YESDEKARGT RLDGLDLVDT WKSFKPRYKH SHFIWNRTEL LTLDPHNVDY LLGLFEPGDM
QYELNRNNVT DPSLSEMVVV AIQILRKNPK GFFLLVEGDR IDHGHHEGKA KQALHEAVEM
DRAIGQAGSL TSSEDTLTVV TADHSHVFTF GGYTPRGNSI FGLAPMLSDT DKKPFTAILY
GNGPGYKVVG GERENVSMVD YAHNNYQAQS AVPLRHETHG GEDVAVFSKG PMAHLLHGVH
EQNYVPHVMA YAACIGANLG HCAPASSAGS LAAGPLLLAL ALYPLSVLF*
speed 0.39 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374830
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.76G>A
g.66372G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -21) | splice site change before start ATG (at aa -20) | splice site change before start ATG (at aa -19) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
117SIGNALmight get lost (downstream of altered splice site)
2929CONFLICTW -> A (in Ref. 10; AA sequence).might get lost (downstream of altered splice site)
6060METALZinc 2 (Potential).might get lost (downstream of altered splice site)
6060METALMagnesium (Potential).might get lost (downstream of altered splice site)
104104CONFLICTN -> K (in Ref. 3; CAA32376).might get lost (downstream of altered splice site)
110110ACT_SITEPhosphoserine intermediate.might get lost (downstream of altered splice site)
140140CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
173173METALMagnesium (Potential).might get lost (downstream of altered splice site)
230230CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 138 / 138
chromosome 1
strand 1
last intron/exon boundary 385
theoretical NMD boundary in CDS 197
length of CDS 513
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 76
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet TGTGGACTACCTATTGGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet TGTGGACTACCTATTGGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
mutated AA sequence N/A
speed 0.49 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

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374829
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.270G>A
g.66372G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -21) | splice site change before start ATG (at aa -20) | splice site change before start ATG (at aa -19) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
117SIGNALmight get lost (downstream of altered splice site)
2929CONFLICTW -> A (in Ref. 10; AA sequence).might get lost (downstream of altered splice site)
6060METALZinc 2 (Potential).might get lost (downstream of altered splice site)
6060METALMagnesium (Potential).might get lost (downstream of altered splice site)
104104CONFLICTN -> K (in Ref. 3; CAA32376).might get lost (downstream of altered splice site)
110110ACT_SITEPhosphoserine intermediate.might get lost (downstream of altered splice site)
140140CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
173173METALMagnesium (Potential).might get lost (downstream of altered splice site)
230230CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 332 / 332
chromosome 1
strand 1
last intron/exon boundary 579
theoretical NMD boundary in CDS 197
length of CDS 513
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 270
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet GCCAGAAACCAGCGGTGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet GCCAGAAACCAGCGGTGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
mutated AA sequence N/A
speed 0.72 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