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 5.22863 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATL1disease_causing_automatic0.999999877677969simple_aaeaffected0L157Wsingle base exchangers119476051show file
ATL1disease_causing_automatic0.999999877677969simple_aaeaffected0L157Wsingle base exchangers119476051show file
ATL1disease_causing_automatic0.999999877677969simple_aaeaffected0L157Wsingle base exchangers119476051show file
ATL1disease_causing_automatic0.999999877677969simple_aaeaffected0L157Wsingle base exchangers119476051show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999877677969 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065473)
  • known disease mutation: rs4353 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51058305T>GN/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.470T>G
cDNA.951T>G
g.59079T>G
AA changes L157W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs119476051
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4353 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4871
4.8431
(flanking)1.1881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained590780.94mu: CAACTTGGAGAGATT ACTT|ggag
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157DTQGTFDSQSTLRDSATVFALSTM
mutated  not conserved    157DTQGTFDSQSTWRDSATVFALST
Ptroglodytes  all identical  ENSPTRG00000023829  157DTQGTFDSQSTLRDSATVFALST
Mmulatta  all identical  ENSMMUG00000009577  146DTQGTFDSQSTLRDSATVFALST
Fcatus  no alignment  ENSFCAG00000006674  n/a
Mmusculus  all identical  ENSMUSG00000021066  157DTQGTFDSQSTLRDSATVFALST
Ggallus  all identical  ENSGALG00000012339  145DTQGTFDSQSTLRDSATVFALST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  158DTQGTFDSQSTLRDSATVFALST
Dmelanogaster  all conserved  FBgn0039213  132FDSQSTVRDCATVFALST
Celegans  all conserved  Y54G2A.2  168DTQGAFDSQSTVKDCATIFALST
Xtropicalis  all identical  ENSXETG00000009126  157DTQGTFDSQSTLRDSATVFALST
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
154170HELIXlost
162162MUTAGENT->P: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
172181STRANDmight get lost (downstream of altered splice site)
184199HELIXmight get lost (downstream of altered splice site)
208219STRANDmight get lost (downstream of altered splice site)
222224TURNmight get lost (downstream of altered splice site)
229241HELIXmight get lost (downstream of altered splice site)
247250STRANDmight get lost (downstream of altered splice site)
253260HELIXmight get lost (downstream of altered splice site)
261270STRANDmight get lost (downstream of altered splice site)
274278HELIXmight get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
291305HELIXmight get lost (downstream of altered splice site)
307309TURNmight get lost (downstream of altered splice site)
322338HELIXmight get lost (downstream of altered splice site)
347375HELIXmight get lost (downstream of altered splice site)
377380STRANDmight get lost (downstream of altered splice site)
384402HELIXmight get lost (downstream of altered splice site)
398398MUTAGENS->Y: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
411437HELIXmight get lost (downstream of altered splice site)
412439COILEDPotential.might get lost (downstream of altered splice site)
448558REGIONSufficient for membrane association.might get lost (downstream of altered splice site)
450470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471471TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
472492TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
493558TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
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 470
cDNA position
(for ins/del: last normal base / first normal base)		 951
gDNA position
(for ins/del: last normal base / first normal base)		 59079
chromosomal position
(for ins/del: last normal base / first normal base)		 51058305
original gDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered gDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
original cDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered cDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
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 FDSQSTWRDS 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*
speed 1.14 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: 0.999999877677969 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065473)
  • known disease mutation: rs4353 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51058305T>GN/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.470T>G
cDNA.711T>G
g.59079T>G
AA changes L157W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs119476051
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4353 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4871
4.8431
(flanking)1.1881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained590780.94mu: CAACTTGGAGAGATT ACTT|ggag
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157DTQGTFDSQSTLRDSATVFALSTM
mutated  not conserved    157DTQGTFDSQSTWRDSATVFALST
Ptroglodytes  all identical  ENSPTRG00000023829  157DTQGTFDSQSTLRDSATVFALST
Mmulatta  all identical  ENSMMUG00000009577  146DTQGTFDSQSTLRDSATVFALST
Fcatus  no alignment  ENSFCAG00000006674  n/a
Mmusculus  all identical  ENSMUSG00000021066  157DTQGTFDSQSTLRDSATVFALST
Ggallus  all identical  ENSGALG00000012339  145DTQGTFDSQSTLRDSATVFALST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  158DTQGTFDSQSTLRDSATVFALST
Dmelanogaster  all conserved  FBgn0039213  132FDSQSTVRDCATVFALST
Celegans  all conserved  Y54G2A.2  168DTQGAFDSQSTVKDCATIFALST
Xtropicalis  all identical  ENSXETG00000009126  157DTQGTFDSQSTLRDSATVFALST
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
154170HELIXlost
162162MUTAGENT->P: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
172181STRANDmight get lost (downstream of altered splice site)
184199HELIXmight get lost (downstream of altered splice site)
208219STRANDmight get lost (downstream of altered splice site)
222224TURNmight get lost (downstream of altered splice site)
229241HELIXmight get lost (downstream of altered splice site)
247250STRANDmight get lost (downstream of altered splice site)
253260HELIXmight get lost (downstream of altered splice site)
261270STRANDmight get lost (downstream of altered splice site)
274278HELIXmight get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
291305HELIXmight get lost (downstream of altered splice site)
307309TURNmight get lost (downstream of altered splice site)
322338HELIXmight get lost (downstream of altered splice site)
347375HELIXmight get lost (downstream of altered splice site)
377380STRANDmight get lost (downstream of altered splice site)
384402HELIXmight get lost (downstream of altered splice site)
398398MUTAGENS->Y: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
411437HELIXmight get lost (downstream of altered splice site)
412439COILEDPotential.might get lost (downstream of altered splice site)
448558REGIONSufficient for membrane association.might get lost (downstream of altered splice site)
450470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471471TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
472492TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
493558TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
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 470
cDNA position
(for ins/del: last normal base / first normal base)		 711
gDNA position
(for ins/del: last normal base / first normal base)		 59079
chromosomal position
(for ins/del: last normal base / first normal base)		 51058305
original gDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered gDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
original cDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered cDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
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 FDSQSTWRDS 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*
speed 1.18 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: 0.999999877677969 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065473)
  • known disease mutation: rs4353 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51058305T>GN/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.470T>G
cDNA.711T>G
g.59079T>G
AA changes L157W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs119476051
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4353 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4871
4.8431
(flanking)1.1881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained590780.94mu: CAACTTGGAGAGATT ACTT|ggag
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157DTQGTFDSQSTLRDSATVFALSTM
mutated  not conserved    157DTQGTFDSQSTWRDSATVFALST
Ptroglodytes  all identical  ENSPTRG00000023829  157DTQGTFDSQSTLRDSATVFALST
Mmulatta  all identical  ENSMMUG00000009577  146DTQGTFDSQSTLRDSATVFALST
Fcatus  no alignment  ENSFCAG00000006674  n/a
Mmusculus  all identical  ENSMUSG00000021066  157DTQGTFDSQSTLRDSATVFALST
Ggallus  all identical  ENSGALG00000012339  145DTQGTFDSQSTLRDSATVFALST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  158DTQGTFDSQSTLRDSATVFALST
Dmelanogaster  all conserved  FBgn0039213  132FDSQSTVRDCATVFALST
Celegans  all conserved  Y54G2A.2  168DTQGAFDSQSTVKDCATIFALST
Xtropicalis  all identical  ENSXETG00000009126  157DTQGTFDSQSTLRDSATVFALST
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
154170HELIXlost
162162MUTAGENT->P: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
172181STRANDmight get lost (downstream of altered splice site)
184199HELIXmight get lost (downstream of altered splice site)
208219STRANDmight get lost (downstream of altered splice site)
222224TURNmight get lost (downstream of altered splice site)
229241HELIXmight get lost (downstream of altered splice site)
247250STRANDmight get lost (downstream of altered splice site)
253260HELIXmight get lost (downstream of altered splice site)
261270STRANDmight get lost (downstream of altered splice site)
274278HELIXmight get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
291305HELIXmight get lost (downstream of altered splice site)
307309TURNmight get lost (downstream of altered splice site)
322338HELIXmight get lost (downstream of altered splice site)
347375HELIXmight get lost (downstream of altered splice site)
377380STRANDmight get lost (downstream of altered splice site)
384402HELIXmight get lost (downstream of altered splice site)
398398MUTAGENS->Y: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
411437HELIXmight get lost (downstream of altered splice site)
412439COILEDPotential.might get lost (downstream of altered splice site)
448558REGIONSufficient for membrane association.might get lost (downstream of altered splice site)
450470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471471TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
472492TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
493558TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
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 470
cDNA position
(for ins/del: last normal base / first normal base)		 711
gDNA position
(for ins/del: last normal base / first normal base)		 59079
chromosomal position
(for ins/del: last normal base / first normal base)		 51058305
original gDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered gDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
original cDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered cDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
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 FDSQSTWRDS 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*
speed 0.48 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: simple_aae, prob: 0.999999877677969 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065473)
  • known disease mutation: rs4353 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51058305T>GN/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.470T>G
cDNA.711T>G
g.59079T>G
AA changes L157W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs119476051
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4353 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065473)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4871
4.8431
(flanking)1.1881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained590780.94mu: CAACTTGGAGAGATT ACTT|ggag
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157DTQGTFDSQSTLRDSATVFALSTM
mutated  not conserved    157DTQGTFDSQSTWRDSATVFALST
Ptroglodytes  all identical  ENSPTRG00000023829  157DTQGTFDSQSTLRDSATVFALST
Mmulatta  all identical  ENSMMUG00000009577  146DTQGTFDSQSTLRDSATVFALST
Fcatus  no alignment  ENSFCAG00000006674  n/a
Mmusculus  all identical  ENSMUSG00000021066  157DTQGTFDSQSTLRDSATVFALST
Ggallus  all identical  ENSGALG00000012339  145DTQGTFDSQSTLRDSATVFALST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  158DTQGTFDSQSTLRDSATVFALST
Dmelanogaster  all conserved  FBgn0039213  132FDSQSTVRDCATVFALST
Celegans  all conserved  Y54G2A.2  168DTQGAFDSQSTVKDCATIFALST
Xtropicalis  all identical  ENSXETG00000009126  157DTQGTFDSQSTLRDSATVFALST
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
154170HELIXlost
162162MUTAGENT->P: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
172181STRANDmight get lost (downstream of altered splice site)
184199HELIXmight get lost (downstream of altered splice site)
208219STRANDmight get lost (downstream of altered splice site)
222224TURNmight get lost (downstream of altered splice site)
229241HELIXmight get lost (downstream of altered splice site)
247250STRANDmight get lost (downstream of altered splice site)
253260HELIXmight get lost (downstream of altered splice site)
261270STRANDmight get lost (downstream of altered splice site)
274278HELIXmight get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
291305HELIXmight get lost (downstream of altered splice site)
307309TURNmight get lost (downstream of altered splice site)
322338HELIXmight get lost (downstream of altered splice site)
347375HELIXmight get lost (downstream of altered splice site)
377380STRANDmight get lost (downstream of altered splice site)
384402HELIXmight get lost (downstream of altered splice site)
398398MUTAGENS->Y: Affects endoplasmic reticulum and Golgi morphology.might get lost (downstream of altered splice site)
411437HELIXmight get lost (downstream of altered splice site)
412439COILEDPotential.might get lost (downstream of altered splice site)
448558REGIONSufficient for membrane association.might get lost (downstream of altered splice site)
450470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471471TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
472492TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
493558TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
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 470
cDNA position
(for ins/del: last normal base / first normal base)		 711
gDNA position
(for ins/del: last normal base / first normal base)		 59079
chromosomal position
(for ins/del: last normal base / first normal base)		 51058305
original gDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered gDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
original cDNA sequence snippet CTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAGTAT
altered cDNA sequence snippet CTTTGATAGTCAGTCAACTTGGAGAGATTCAGCCACAGTAT
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 FDSQSTWRDS 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*
speed 1.36 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