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 6.020957 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALPLdisease_causing_automatic0.999996488940009simple_aae0A33Vsingle base exchangers121918005show file
ALPLdisease_causing_automatic0.999996488940009simple_aae0A33Vsingle base exchangers121918005show file
ALPLdisease_causing_automatic0.999996488940009simple_aae0A33Vsingle base exchangers121918005show file
ALPLdisease_causing_automatic1without_aae0single base exchangers121918005show file
ALPLdisease_causing_automatic1without_aae0single base exchangers121918005show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999996488940009 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920016)
  • known disease mutation: rs13667 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/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.98C>T
cDNA.348C>T
g.51298C>T
AA changes A33V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
33
frameshift no
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC
 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG
 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG
 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33KEKDPKYWRDQAQETLKYALELQK
mutated  not conserved    33KEKDPKYWRDQVQETLKYALELQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  33KEKDPKYWRDQAQETLKYALELQ
Fcatus  all identical  ENSFCAG00000002960  33KEKDPKYWRDQAQQTLKNALRLQ
Mmusculus  all identical  ENSMUSG00000028766  33KERDPSYWRQQAQETLKNALKLQ
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  34QEKDPKFWNTWAQQTLKNALSLQ
Drerio  all identical  ENSDARG00000015546  65QEKRPDYWRDFAQRSLKDALKLQ
Dmelanogaster  all identical  FBgn0043791  73EERYAEYWQGLAAQTLDQQLESKL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
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 98
cDNA position
(for ins/del: last normal base / first normal base)
348
gDNA position
(for ins/del: last normal base / first normal base)
51298
chromosomal position
(for ins/del: last normal base / first normal base)
21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 DQVQETLKYA 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*
speed 1.43 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: 0.999996488940009 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920016)
  • known disease mutation: rs13667 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/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.98C>T
cDNA.352C>T
g.51298C>T
AA changes A33V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
33
frameshift no
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC
 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG
 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG
 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33KEKDPKYWRDQAQETLKYALELQK
mutated  not conserved    33KEKDPKYWRDQVQETLKYALELQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  33KEKDPKYWRDQAQETLKYALELQ
Fcatus  all identical  ENSFCAG00000002960  33KEKDPKYWRDQAQQTLKNALRLQ
Mmusculus  all identical  ENSMUSG00000028766  33KERDPSYWRQQAQETLKNALKLQ
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  34QEKDPKFWNTWAQQTLKNALSLQ
Drerio  all identical  ENSDARG00000015546  65QEKRPDYWRDFAQRSLKDALKLQ
Dmelanogaster  all identical  FBgn0043791  73EERYAEYWQGLAAQTLDQQLESKL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
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 98
cDNA position
(for ins/del: last normal base / first normal base)
352
gDNA position
(for ins/del: last normal base / first normal base)
51298
chromosomal position
(for ins/del: last normal base / first normal base)
21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 DQVQETLKYA 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*
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: simple_aae, prob: 0.999996488940009 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920016)
  • known disease mutation: rs13667 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/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.98C>T
cDNA.98C>T
g.51298C>T
AA changes A33V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
33
frameshift no
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC
 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG
 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG
 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33KEKDPKYWRDQAQETLKYALELQK
mutated  not conserved    33KEKDPKYWRDQVQETLKYALELQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  33KEKDPKYWRDQAQETLKYALELQ
Fcatus  all identical  ENSFCAG00000002960  33KEKDPKYWRDQAQQTLKNALRLQ
Mmusculus  all identical  ENSMUSG00000028766  33KERDPSYWRQQAQETLKNALKLQ
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  34QEKDPKFWNTWAQQTLKNALSLQ
Drerio  all identical  ENSDARG00000015546  65QEKRPDYWRDFAQRSLKDALKLQ
Dmelanogaster  all identical  FBgn0043791  73EERYAEYWQGLAAQTLDQQLESKL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
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 98
cDNA position
(for ins/del: last normal base / first normal base)
98
gDNA position
(for ins/del: last normal base / first normal base)
51298
chromosomal position
(for ins/del: last normal base / first normal base)
21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 DQVQETLKYA 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*
speed 1.40 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 CM920016)
  • known disease mutation: rs13667 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000540617
Genbank transcript ID NM_001127501
UniProt peptide N/A
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.190C>T
g.51298C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC
 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG
 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG
 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes
N/A
protein features N/A
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 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 N/A
cDNA position
(for ins/del: last normal base / first normal base)
190
gDNA position
(for ins/del: last normal base / first normal base)
51298
chromosomal position
(for ins/del: last normal base / first normal base)
21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 N/A
speed 0.35 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
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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 CM920016)
  • known disease mutation: rs13667 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000539907
Genbank transcript ID NM_001177520
UniProt peptide N/A
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.190C>T
g.51298C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC
 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG
 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG
 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes
N/A
protein features N/A
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 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 N/A
cDNA position
(for ins/del: last normal base / first normal base)
190
gDNA position
(for ins/del: last normal base / first normal base)
51298
chromosomal position
(for ins/del: last normal base / first normal base)
21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 N/A
speed 1.13 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
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Problems