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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000374840
Querying Taster for transcript #2: ENST00000374832
Querying Taster for transcript #3: ENST00000425315
Querying Taster for transcript #4: ENST00000539907
Querying Taster for transcript #5: ENST00000540617
MT speed 0 s - this script 4.445704 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALPLdisease_causing_automatic0.999992904591756simple_aaeaffected0R136Hsingle base exchangers121918011show file
ALPLdisease_causing_automatic0.999992904591756simple_aaeaffected0R136Hsingle base exchangers121918011show file
ALPLdisease_causing_automatic0.999992904591756simple_aaeaffected0R136Hsingle base exchangers121918011show file
ALPLdisease_causing_automatic0.999992904591756simple_aaeaffected0R59Hsingle base exchangers121918011show file
ALPLdisease_causing_automatic0.999992904591756simple_aaeaffected0R81Hsingle base exchangers121918011show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999992904591756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM127629)
  • known disease mutation at this position (HGMD CM138789)
  • known disease mutation at this position (HGMD CM980062)
  • known disease mutation: rs13675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889712G>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.407G>A
cDNA.657G>A
g.53855G>A
AA changes R136H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 136
frameshift no
known variant Reference ID: rs121918011
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs13675 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7820.997
5.2230.997
(flanking)-0.2130.227
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53847wt: 0.40 / mu: 0.47wt: GCAGCCACTGAGCGT
mu: GCAGCCACTGAGCAT		 AGCC|actg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      136EGTVGVSAATERSRCNTTQGNEVT
mutated  not conserved    136EGTVGVSAATEHSRCNTTQGNEV
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  136EGTVGVSAATERSRCNTTQGNEV
Fcatus  all identical  ENSFCAG00000002960  136EGTVGVSAATQRTQCNTTQGNEV
Mmusculus  all identical  ENSMUSG00000028766  136EGTVGVSAATERTRCNTTQGNEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  137AAVRSQCNTTKGNEV
Drerio  all identical  ENSDARG00000015546  173EGTVGVSAAAVRSQCNTTQGNEV
Dmelanogaster  not conserved  FBgn0043791  175YGTIGVSAAVQFKDCQAQAQAAH
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 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 407
cDNA position
(for ins/del: last normal base / first normal base)		 657
gDNA position
(for ins/del: last normal base / first normal base)		 53855
chromosomal position
(for ins/del: last normal base / first normal base)		 21889712
original gDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered gDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
original cDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered cDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
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 SAATEHSRCN 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*
speed 0.78 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: 0.999992904591756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM127629)
  • known disease mutation at this position (HGMD CM138789)
  • known disease mutation at this position (HGMD CM980062)
  • known disease mutation: rs13675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889712G>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.407G>A
cDNA.661G>A
g.53855G>A
AA changes R136H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 136
frameshift no
known variant Reference ID: rs121918011
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs13675 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7820.997
5.2230.997
(flanking)-0.2130.227
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53847wt: 0.40 / mu: 0.47wt: GCAGCCACTGAGCGT
mu: GCAGCCACTGAGCAT		 AGCC|actg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      136EGTVGVSAATERSRCNTTQGNEVT
mutated  not conserved    136EGTVGVSAATEHSRCNTTQGNEV
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  136EGTVGVSAATERSRCNTTQGNEV
Fcatus  all identical  ENSFCAG00000002960  136EGTVGVSAATQRTQCNTTQGNEV
Mmusculus  all identical  ENSMUSG00000028766  136EGTVGVSAATERTRCNTTQGNEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  137AAVRSQCNTTKGNEV
Drerio  all identical  ENSDARG00000015546  173EGTVGVSAAAVRSQCNTTQGNEV
Dmelanogaster  not conserved  FBgn0043791  175YGTIGVSAAVQFKDCQAQAQAAH
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 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 407
cDNA position
(for ins/del: last normal base / first normal base)		 661
gDNA position
(for ins/del: last normal base / first normal base)		 53855
chromosomal position
(for ins/del: last normal base / first normal base)		 21889712
original gDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered gDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
original cDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered cDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
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 SAATEHSRCN 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*
speed 0.51 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: 0.999992904591756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM127629)
  • known disease mutation at this position (HGMD CM138789)
  • known disease mutation at this position (HGMD CM980062)
  • known disease mutation: rs13675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889712G>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.407G>A
cDNA.407G>A
g.53855G>A
AA changes R136H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 136
frameshift no
known variant Reference ID: rs121918011
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs13675 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7820.997
5.2230.997
(flanking)-0.2130.227
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53847wt: 0.40 / mu: 0.47wt: GCAGCCACTGAGCGT
mu: GCAGCCACTGAGCAT		 AGCC|actg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      136EGTVGVSAATERSRCNTTQGNEVT
mutated  not conserved    136EGTVGVSAATEHSRCNTTQGNEV
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  136EGTVGVSAATERSRCNTTQGNEV
Fcatus  all identical  ENSFCAG00000002960  136EGTVGVSAATQRTQCNTTQGNEV
Mmusculus  all identical  ENSMUSG00000028766  136EGTVGVSAATERTRCNTTQGNEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  137AAVRSQCNTTKGNEV
Drerio  all identical  ENSDARG00000015546  173EGTVGVSAAAVRSQCNTTQGNEV
Dmelanogaster  not conserved  FBgn0043791  175YGTIGVSAAVQFKDCQAQAQAAH
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 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 407
cDNA position
(for ins/del: last normal base / first normal base)		 407
gDNA position
(for ins/del: last normal base / first normal base)		 53855
chromosomal position
(for ins/del: last normal base / first normal base)		 21889712
original gDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered gDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
original cDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered cDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
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 SAATEHSRCN 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*
speed 0.61 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: 0.999992904591756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM127629)
  • known disease mutation at this position (HGMD CM138789)
  • known disease mutation at this position (HGMD CM980062)
  • known disease mutation: rs13675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889712G>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.176G>A
cDNA.383G>A
g.53855G>A
AA changes R59H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 59
frameshift no
known variant Reference ID: rs121918011
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs13675 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7820.997
5.2230.997
(flanking)-0.2130.227
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53847wt: 0.40 / mu: 0.47wt: GCAGCCACTGAGCGT
mu: GCAGCCACTGAGCAT		 AGCC|actg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      59EGTVGVSAATERSRCNTTQGNEVT
mutated  not conserved    59EGTVGVSAATEHSRCNTTQGNEV
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  136EGTVGVSAATERSRCNTTQGNEV
Fcatus  all identical  ENSFCAG00000002960  136EGTVGVSAATQRTQCNTTQGNEV
Mmusculus  all identical  ENSMUSG00000028766  136EGTVGVSAATERTRCNTTQGNEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  134EGTVGVSAAAVRS
Drerio  all identical  ENSDARG00000015546  173EGTVGVSAAAVRSQCNTTQGNEV
Dmelanogaster  not conserved  FBgn0043791  171YGTIGVSAAVQFKDCQAQAQAAHHV
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
6060METALMagnesium (Potential).might get lost (downstream of altered splice site)
6060METALZinc 2 (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 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 176
cDNA position
(for ins/del: last normal base / first normal base)		 383
gDNA position
(for ins/del: last normal base / first normal base)		 53855
chromosomal position
(for ins/del: last normal base / first normal base)		 21889712
original gDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered gDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
original cDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered cDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
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 VGVSAATEHS
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*
speed 0.76 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: 0.999992904591756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM127629)
  • known disease mutation at this position (HGMD CM138789)
  • known disease mutation at this position (HGMD CM980062)
  • known disease mutation: rs13675 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889712G>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.242G>A
cDNA.499G>A
g.53855G>A
AA changes R81H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 81
frameshift no
known variant Reference ID: rs121918011
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02424

known disease mutation: rs13675 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127629)
known disease mutation at this position, please check HGMD for details (HGMD ID CM138789)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7820.997
5.2230.997
(flanking)-0.2130.227
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53847wt: 0.40 / mu: 0.47wt: GCAGCCACTGAGCGT
mu: GCAGCCACTGAGCAT		 AGCC|actg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      81EGTVGVSAATERSRCNTTQGNEVT
mutated  not conserved    81EGTVGVSAATEHSRCNTTQGNEV
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  136EGTVGVSAATERSRCNTTQGNEV
Fcatus  all identical  ENSFCAG00000002960  136EGTVGVSAATQRTQCNTTQGNEV
Mmusculus  all identical  ENSMUSG00000028766  136EGTVGVSAATERTRCNTTQGNEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  137EGTVGVSAAAVRSQCNTTKGNEV
Drerio  all identical  ENSDARG00000015546  173EGTVGVSAAAVRSQCNTTQGNEV
Dmelanogaster  not conserved  FBgn0043791  171YGTIGVSAAVQFKDCQAQAQAAHHV
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 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 242
cDNA position
(for ins/del: last normal base / first normal base)		 499
gDNA position
(for ins/del: last normal base / first normal base)		 53855
chromosomal position
(for ins/del: last normal base / first normal base)		 21889712
original gDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered gDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
original cDNA sequence snippet GGTAAGCGCAGCCACTGAGCGTTCCCGGTGCAACACCACCC
altered cDNA sequence snippet GGTAAGCGCAGCCACTGAGCATTCCCGGTGCAACACCACCC
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 HSRCNTTQGN 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*
speed 0.65 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