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 4.32 s - this script 5.264428 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALPLdisease_causing_automatic0.99999999999041simple_aaeaffected0D24Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.99999999999041simple_aaeaffected0D24Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.99999999999041simple_aaeaffected0D301Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.99999999999041simple_aaeaffected0D323Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.9999999999995simple_aaeaffected0D378Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.9999999999995simple_aaeaffected0D378Vsingle base exchangers121918008show file
ALPLdisease_causing_automatic0.9999999999995simple_aaeaffected0D378Vsingle base exchangers121918008show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999041 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>TN/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 CDS
DNA changes c.71A>T
cDNA.208A>T
g.66504A>T
AA changes D24V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 24
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      24SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    24SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378SIHDTLTIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412STDDTLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 513 / 513
position (AA) of stopcodon in wt / mu AA sequence 171 / 171
position of stopcodon in wt / mu cDNA 650 / 650
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 71
cDNA position
(for ins/del: last normal base / first normal base)		 208
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
wildtype AA sequence MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
mutated AA sequence MDRAIGQAGS LTSSEDTLTV VTAVHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999041 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>TN/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 CDS
DNA changes c.71A>T
cDNA.402A>T
g.66504A>T
AA changes D24V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 24
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      24SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    24SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378SIHDTLTIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412STDDTLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 513 / 513
position (AA) of stopcodon in wt / mu AA sequence 171 / 171
position of stopcodon in wt / mu cDNA 844 / 844
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 71
cDNA position
(for ins/del: last normal base / first normal base)		 402
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
wildtype AA sequence MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
mutated AA sequence MDRAIGQAGS LTSSEDTLTV VTAVHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
speed 0.60 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: 0.99999999999041 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>TN/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.902A>T
cDNA.1109A>T
g.66504A>T
AA changes D301V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 301
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      301SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    301VHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378DHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412STDDTLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 902
cDNA position
(for ins/del: last normal base / first normal base)		 1109
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
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 FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
VHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
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: 0.99999999999041 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>TN/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.968A>T
cDNA.1225A>T
g.66504A>T
AA changes D323V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 323
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      323SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    323SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378SIHDTLTIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412STDDTLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 968
cDNA position
(for ins/del: last normal base / first normal base)		 1225
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
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 GFFLLVEGGR IDHGHHEGKA KQALHEAVEM
DRAIGQAGSL TSSEDTLTVV TAVHSHVFTF GGYTPRGNSI FGLAPMLSDT DKKPFTAILY
GNGPGYKVVG GERENVSMVD YAHNNYQAQS AVPLRHETHG GEDVAVFSKG PMAHLLHGVH
EQNYVPHVMA YAACIGANLG HCAPASSAGS LAAGPLLLAL ALYPLSVLF*
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: 0.9999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>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.1133A>T
cDNA.1383A>T
g.66504A>T
AA changes D378V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 378
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      378SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    378SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378TIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412TLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
378378METALZinc 2 (Potential).lost
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 1133
cDNA position
(for ins/del: last normal base / first normal base)		 1383
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
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 VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTAVHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 0.45 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: 0.9999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>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.1133A>T
cDNA.1387A>T
g.66504A>T
AA changes D378V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 378
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      378SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    378SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378TIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412TLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
378378METALZinc 2 (Potential).lost
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 1133
cDNA position
(for ins/del: last normal base / first normal base)		 1387
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
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 VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTAVHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 0.81 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: 0.9999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM172360)
  • known disease mutation at this position (HGMD CM920022)
  • known disease mutation: rs13671 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902361A>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.1133A>T
cDNA.1133A>T
g.66504A>T
AA changes D378V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 378
frameshift no
known variant Reference ID: rs121918008
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13671 (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 CM172360)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920022)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
4.3421
(flanking)0.9631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66514wt: 0.33 / mu: 0.71wt: GTCACTGCGGACCATTCCCACGTCTTCACATTTGGTGGATA
mu: GTCACTGCGGTCCATTCCCACGTCTTCACATTTGGTGGATA		 ccac|GTCT
Donor marginally increased66509wt: 0.9078 / mu: 0.9280 (marginal change - not scored)wt: ACCATTCCCACGTCT
mu: TCCATTCCCACGTCT		 CATT|ccca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      378SSEDTLTVVTADHSHVFTFGGYTP
mutated  not conserved    378SSEDTLTVVTAVHSHVFTFGGYT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  378SLEDTLTVVTADHSHVFTFGGYT
Fcatus  all identical  ENSFCAG00000002960  378SVEDTLTIVTADHSHVFTFGGYT
Mmusculus  all identical  ENSMUSG00000028766  378SQKDTLTVVTADHSHVFTFGGYT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  378TIVTADHSHVFNFGGYT
Drerio  all identical  ENSDARG00000015546  414SEYDTLTVVTADHSHVFSFGGYT
Dmelanogaster  all identical  FBgn0043791  412TLIVVSSDHSHTMSLAGYS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
378378METALZinc 2 (Potential).lost
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 1133
cDNA position
(for ins/del: last normal base / first normal base)		 1133
gDNA position
(for ins/del: last normal base / first normal base)		 66504
chromosomal position
(for ins/del: last normal base / first normal base)		 21902361
original gDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered gDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
original cDNA sequence snippet TCTGACCGTGGTCACTGCGGACCATTCCCACGTCTTCACAT
altered cDNA sequence snippet TCTGACCGTGGTCACTGCGGTCCATTCCCACGTCTTCACAT
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 VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTAVHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
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

Problems