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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000441560
Querying Taster for transcript #2: ENST00000358385
Querying Taster for transcript #3: ENST00000357032
Querying Taster for transcript #4: ENST00000354525
MT speed 0 s - this script 3.930978 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATL1disease_causing_automatic0.999999989936005simple_aae0S259Ysingle base exchangers119476047show file
ATL1disease_causing_automatic0.999999989936005simple_aae0S259Ysingle base exchangers119476047show file
ATL1disease_causing_automatic0.999999989936005simple_aae0S259Ysingle base exchangers119476047show file
ATL1disease_causing_automatic0.999999989936005simple_aae0S259Ysingle base exchangers119476047show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999989936005 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013292)
  • known disease mutation at this position (HGMD CM092579)
  • known disease mutation: rs4347 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51081143C>AN/A show variant in all transcripts   IGV
HGNC symbol ATL1
Ensembl transcript ID ENST00000441560
Genbank transcript ID NM_001127713
UniProt peptide Q8WXF7
alteration type single base exchange
alteration region CDS
DNA changes c.776C>A
cDNA.1257C>A
g.81917C>A
AA changes S259Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 259
frameshift no
known variant Reference ID: rs119476047
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4347 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3961
4.3081
(flanking)1.7171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259EELQNVRKHIHSCFTNISCFLLPH
mutated  not conserved    259EELQNVRKHIHYCFTNISCFLLP
Ptroglodytes  all identical  ENSPTRG00000023829  259EELQNVRKHIHSCFTNISCFLLP
Mmulatta  all identical  ENSMMUG00000009577  248NVRKHIHSCFTNISCFLLP
Fcatus  not conserved  ENSFCAG00000006674  67XXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000021066  259EELQNVRKHIHSCFTNISCFLLP
Ggallus  all identical  ENSGALG00000012339  247RKHIHSCFTKISCFLLP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  260EELQNVRKHIHSCFTNISCFLMP
Dmelanogaster  all identical  FBgn0039213  234PELQSLRRHISSCFTEVACFLMP
Celegans  all identical  Y54G2A.2  270AELQQLRQHIRSCFED
Xtropicalis  all identical  ENSXETG00000009126  259EELQNVRKHIHSCFTNISCFLMP
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
253260HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1662 / 1662
position (AA) of stopcodon in wt / mu AA sequence 554 / 554
position of stopcodon in wt / mu cDNA 2143 / 2143
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 482 / 482
chromosome 14
strand 1
last intron/exon boundary 2033
theoretical NMD boundary in CDS 1501
length of CDS 1662
coding sequence (CDS) position 776
cDNA position
(for ins/del: last normal base / first normal base)		 1257
gDNA position
(for ins/del: last normal base / first normal base)		 81917
chromosomal position
(for ins/del: last normal base / first normal base)		 51081143
original gDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered gDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
original cDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered cDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
wildtype AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
mutated AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHYC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
speed 1.03 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999989936005 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013292)
  • known disease mutation at this position (HGMD CM092579)
  • known disease mutation: rs4347 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51081143C>AN/A show variant in all transcripts   IGV
HGNC symbol ATL1
Ensembl transcript ID ENST00000358385
Genbank transcript ID NM_015915
UniProt peptide Q8WXF7
alteration type single base exchange
alteration region CDS
DNA changes c.776C>A
cDNA.1017C>A
g.81917C>A
AA changes S259Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 259
frameshift no
known variant Reference ID: rs119476047
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4347 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3961
4.3081
(flanking)1.7171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259EELQNVRKHIHSCFTNISCFLLPH
mutated  not conserved    259EELQNVRKHIHYCFTNISCFLLP
Ptroglodytes  all identical  ENSPTRG00000023829  259EELQNVRKHIHSCFTNISCFLLP
Mmulatta  all identical  ENSMMUG00000009577  248NVRKHIHSCFTNISCFLLP
Fcatus  not conserved  ENSFCAG00000006674  67XXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000021066  259EELQNVRKHIHSCFTNISCFLLP
Ggallus  all identical  ENSGALG00000012339  247RKHIHSCFTKISCFLLP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  260EELQNVRKHIHSCFTNISCFLMP
Dmelanogaster  all identical  FBgn0039213  234PELQSLRRHISSCFTEVACFLMP
Celegans  all identical  Y54G2A.2  270AELQQLRQHIRSCFED
Xtropicalis  all identical  ENSXETG00000009126  259EELQNVRKHIHSCFTNISCFLMP
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
253260HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1677 / 1677
position (AA) of stopcodon in wt / mu AA sequence 559 / 559
position of stopcodon in wt / mu cDNA 1918 / 1918
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 242 / 242
chromosome 14
strand 1
last intron/exon boundary 1808
theoretical NMD boundary in CDS 1516
length of CDS 1677
coding sequence (CDS) position 776
cDNA position
(for ins/del: last normal base / first normal base)		 1017
gDNA position
(for ins/del: last normal base / first normal base)		 81917
chromosomal position
(for ins/del: last normal base / first normal base)		 51081143
original gDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered gDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
original cDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered cDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
wildtype AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGST NEALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*
mutated AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHYC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGST NEALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*
speed 0.44 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: 0.999999989936005 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013292)
  • known disease mutation at this position (HGMD CM092579)
  • known disease mutation: rs4347 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51081143C>AN/A show variant in all transcripts   IGV
HGNC symbol ATL1
Ensembl transcript ID ENST00000357032
Genbank transcript ID N/A
UniProt peptide Q8WXF7
alteration type single base exchange
alteration region CDS
DNA changes c.776C>A
cDNA.1017C>A
g.81917C>A
AA changes S259Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 259
frameshift no
known variant Reference ID: rs119476047
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4347 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3961
4.3081
(flanking)1.7171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259EELQNVRKHIHSCFTNISCFLLPH
mutated  not conserved    259EELQNVRKHIHYCFTNISCFLLP
Ptroglodytes  all identical  ENSPTRG00000023829  259EELQNVRKHIHSCFTNISCFLLP
Mmulatta  all identical  ENSMMUG00000009577  248NVRKHIHSCFTNISCFLLP
Fcatus  not conserved  ENSFCAG00000006674  67XXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000021066  259EELQNVRKHIHSCFTNISCFLLP
Ggallus  all identical  ENSGALG00000012339  247RKHIHSCFTKISCFLLP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  260EELQNVRKHIHSCFTNISCFLMP
Dmelanogaster  all identical  FBgn0039213  234PELQSLRRHISSCFTEVACFLMP
Celegans  all identical  Y54G2A.2  270AELQQLRQHIRSCFED
Xtropicalis  all identical  ENSXETG00000009126  259EELQNVRKHIHSCFTNISCFLMP
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
253260HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1677 / 1677
position (AA) of stopcodon in wt / mu AA sequence 559 / 559
position of stopcodon in wt / mu cDNA 1918 / 1918
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 242 / 242
chromosome 14
strand 1
last intron/exon boundary 1808
theoretical NMD boundary in CDS 1516
length of CDS 1677
coding sequence (CDS) position 776
cDNA position
(for ins/del: last normal base / first normal base)		 1017
gDNA position
(for ins/del: last normal base / first normal base)		 81917
chromosomal position
(for ins/del: last normal base / first normal base)		 51081143
original gDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered gDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
original cDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered cDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
wildtype AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGPS HQALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*
mutated AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHYC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGPS HQALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*
speed 0.43 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: 0.999999989936005 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013292)
  • known disease mutation at this position (HGMD CM092579)
  • known disease mutation: rs4347 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51081143C>AN/A show variant in all transcripts   IGV
HGNC symbol ATL1
Ensembl transcript ID ENST00000354525
Genbank transcript ID NM_181598
UniProt peptide Q8WXF7
alteration type single base exchange
alteration region CDS
DNA changes c.776C>A
cDNA.1017C>A
g.81917C>A
AA changes S259Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 259
frameshift no
known variant Reference ID: rs119476047
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4347 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013292)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092579)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3961
4.3081
(flanking)1.7171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259EELQNVRKHIHSCFTNISCFLLPH
mutated  not conserved    259EELQNVRKHIHYCFTNISCFLLP
Ptroglodytes  all identical  ENSPTRG00000023829  259EELQNVRKHIHSCFTNISCFLLP
Mmulatta  all identical  ENSMMUG00000009577  248NVRKHIHSCFTNISCFLLP
Fcatus  not conserved  ENSFCAG00000006674  67XXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000021066  259EELQNVRKHIHSCFTNISCFLLP
Ggallus  all identical  ENSGALG00000012339  247RKHIHSCFTKISCFLLP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  260EELQNVRKHIHSCFTNISCFLMP
Dmelanogaster  all identical  FBgn0039213  234PELQSLRRHISSCFTEVACFLMP
Celegans  all identical  Y54G2A.2  270AELQQLRQHIRSCFED
Xtropicalis  all identical  ENSXETG00000009126  259EELQNVRKHIHSCFTNISCFLMP
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
253260HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1662 / 1662
position (AA) of stopcodon in wt / mu AA sequence 554 / 554
position of stopcodon in wt / mu cDNA 1903 / 1903
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 242 / 242
chromosome 14
strand 1
last intron/exon boundary 1793
theoretical NMD boundary in CDS 1501
length of CDS 1662
coding sequence (CDS) position 776
cDNA position
(for ins/del: last normal base / first normal base)		 1017
gDNA position
(for ins/del: last normal base / first normal base)		 81917
chromosomal position
(for ins/del: last normal base / first normal base)		 51081143
original gDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered gDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
original cDNA sequence snippet CGTCAGAAAACACATCCATTCCTGTTTCACCAACATTTCCT
altered cDNA sequence snippet CGTCAGAAAACACATCCATTACTGTTTCACCAACATTTCCT
wildtype AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
mutated AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHYC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
speed 0.43 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
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Problems