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: ENST00000290597
Querying Taster for transcript #2: ENST00000375341
Querying Taster for transcript #3: ENST00000538839
Querying Taster for transcript #4: ENST00000538309
MT speed 0 s - this script 4.792684 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALDH4A1disease_causing_automatic0.999999997781199simple_aaeaffected0S352Lsingle base exchangers137852937show file
ALDH4A1disease_causing_automatic0.999999999838259simple_aaeaffected0S352Lsingle base exchangers137852937show file
ALDH4A1disease_causing_automatic0.999999999838259simple_aaeaffected0S352Lsingle base exchangers137852937show file
ALDH4A1disease_causing_automatic0.999999999879803simple_aaeaffected0S292Lsingle base exchangers137852937show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997781199 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980054)
  • known disease mutation: rs4003 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:19203992G>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH4A1
Ensembl transcript ID ENST00000538839
Genbank transcript ID N/A
UniProt peptide P30038
alteration type single base exchange
alteration region CDS
DNA changes c.1055C>T
cDNA.1060C>T
g.25284C>T
AA changes S352L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 352
frameshift no
known variant Reference ID: rs137852937
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs4003 (pathogenic for Deficiency of pyrroline-5-carboxylate reductase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2790.964
4.9231
(flanking)4.081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased25286wt: 0.36 / mu: 0.56wt: AGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCG
mu: AGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCG		 tcgc|GTCT
Acc increased25292wt: 0.30 / mu: 0.43wt: GTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCGCTGTGG
mu: GTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCGCTGTGG		 ctct|ACGT
Donor marginally increased25289wt: 0.6604 / mu: 0.6873 (marginal change - not scored)wt: CGCGTCTCTACGTGC
mu: TGCGTCTCTACGTGC		 CGTC|tcta
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352FEYGGQKCSACSRLYVPHSLWPQI
mutated  not conserved    352FEYGGQKCSACLRLYVPHSL
Ptroglodytes  all identical  ENSPTRG00000000255  352FEYGGQKCSACSRLYVPHSL
Mmulatta  all identical  ENSMMUG00000004751  219FEYGGQKCSACSRLYVPHSLWPQ
Fcatus  all identical  ENSFCAG00000008767  351FEYGGQKCSACSRLYVPQSL
Mmusculus  all identical  ENSMUSG00000028737  351FEYGGQKCSACSRLYVPKSLW
Ggallus  all identical  ENSGALG00000003804  340FEYGGQKCSACSRLYAPRSLWPQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000038207  345FEYGGQKCSACSRMYVPDSLWPQ
Dmelanogaster  all identical  FBgn0037138  363FEYCGQKCSACSRMYVPESLWPQ
Celegans  all identical  F56D12.1  352WEYSGQKCSACSRMYAPKSIWPK
Xtropicalis  no alignment  ENSXETG00000018531  n/a
protein features
start (aa)end (aa)featuredetails 
351357STRANDlost
352352MUTAGENS->A: Reduced affinity for NAD. No effect on enzyme activity.lost
354354CONFLICTL -> K (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
358360HELIXmight get lost (downstream of altered splice site)
361373HELIXmight get lost (downstream of altered splice site)
376376CONFLICTK -> R (in Ref. 3; BAD96206).might get lost (downstream of altered splice site)
380382TURNmight get lost (downstream of altered splice site)
394409HELIXmight get lost (downstream of altered splice site)
402402MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
413417STRANDmight get lost (downstream of altered splice site)
424426STRANDmight get lost (downstream of altered splice site)
432437STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
447447BINDINGNAD (By similarity).might get lost (downstream of altered splice site)
450458STRANDmight get lost (downstream of altered splice site)
460462HELIXmight get lost (downstream of altered splice site)
463473HELIXmight get lost (downstream of altered splice site)
474483STRANDmight get lost (downstream of altered splice site)
487496HELIXmight get lost (downstream of altered splice site)
497500TURNmight get lost (downstream of altered splice site)
502508STRANDmight get lost (downstream of altered splice site)
505505MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
513513BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
515517TURNmight get lost (downstream of altered splice site)
524526CONFLICTRAS -> GSA (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
534536STRANDmight get lost (downstream of altered splice site)
537541HELIXmight get lost (downstream of altered splice site)
542550STRANDmight get lost (downstream of altered splice site)
560562HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1539 / 1539
position (AA) of stopcodon in wt / mu AA sequence 513 / 513
position of stopcodon in wt / mu cDNA 1544 / 1544
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 6 / 6
chromosome 1
strand -1
last intron/exon boundary 1432
theoretical NMD boundary in CDS 1376
length of CDS 1539
coding sequence (CDS) position 1055
cDNA position
(for ins/del: last normal base / first normal base)		 1060
gDNA position
(for ins/del: last normal base / first normal base)		 25284
chromosomal position
(for ins/del: last normal base / first normal base)		 19203992
original gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
original cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
wildtype AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CSRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKEIFGP VLSVYVYPDD KYKETLQLVD
STTSYGLTGA VFSQDKDVVQ EATKVLRNAA GNFYINDKST GSIVGQQPFG GARASGTNDK
PGGPHYILRW TSPQVIKETH KPLGDWSYAY MQ*
mutated AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CLRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKEIFGP VLSVYVYPDD KYKETLQLVD
STTSYGLTGA VFSQDKDVVQ EATKVLRNAA GNFYINDKST GSIVGQQPFG GARASGTNDK
PGGPHYILRW TSPQVIKETH KPLGDWSYAY MQ*
speed 0.84 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: 0.999999999838259 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980054)
  • known disease mutation: rs4003 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:19203992G>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH4A1
Ensembl transcript ID ENST00000290597
Genbank transcript ID NM_170726
UniProt peptide P30038
alteration type single base exchange
alteration region CDS
DNA changes c.1055C>T
cDNA.1085C>T
g.25284C>T
AA changes S352L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 352
frameshift no
known variant Reference ID: rs137852937
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs4003 (pathogenic for Deficiency of pyrroline-5-carboxylate reductase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2790.964
4.9231
(flanking)4.081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased25286wt: 0.36 / mu: 0.56wt: AGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCG
mu: AGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCG		 tcgc|GTCT
Acc increased25292wt: 0.30 / mu: 0.43wt: GTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCGCTGTGG
mu: GTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCGCTGTGG		 ctct|ACGT
Donor marginally increased25289wt: 0.6604 / mu: 0.6873 (marginal change - not scored)wt: CGCGTCTCTACGTGC
mu: TGCGTCTCTACGTGC		 CGTC|tcta
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352FEYGGQKCSACSRLYVPHSLWPQI
mutated  not conserved    352FEYGGQKCSACLRLYVPHSL
Ptroglodytes  all identical  ENSPTRG00000000255  352FEYGGQKCSACSRLYVPHSL
Mmulatta  all identical  ENSMMUG00000004751  219FEYGGQKCSACSRLYVPHSLWPQ
Fcatus  all identical  ENSFCAG00000008767  351FEYGGQKCSACSRLYVPQSL
Mmusculus  all identical  ENSMUSG00000028737  351FEYGGQKCSACSRLYVPKSLW
Ggallus  all identical  ENSGALG00000003804  340FEYGGQKCSACSRLYAPRSLWPQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000038207  345FEYGGQKCSACSRMYVPDSLWPQ
Dmelanogaster  all identical  FBgn0037138  363FEYCGQKCSACSRMYVPESLWPQ
Celegans  all identical  F56D12.1  352WEYSGQKCSACSRMYAPKSIWPK
Xtropicalis  all identical  ENSXETG00000018531  326METVGQ--DGDSRARWRHRTRWR
protein features
start (aa)end (aa)featuredetails 
351357STRANDlost
352352MUTAGENS->A: Reduced affinity for NAD. No effect on enzyme activity.lost
354354CONFLICTL -> K (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
358360HELIXmight get lost (downstream of altered splice site)
361373HELIXmight get lost (downstream of altered splice site)
376376CONFLICTK -> R (in Ref. 3; BAD96206).might get lost (downstream of altered splice site)
380382TURNmight get lost (downstream of altered splice site)
394409HELIXmight get lost (downstream of altered splice site)
402402MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
413417STRANDmight get lost (downstream of altered splice site)
424426STRANDmight get lost (downstream of altered splice site)
432437STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
447447BINDINGNAD (By similarity).might get lost (downstream of altered splice site)
450458STRANDmight get lost (downstream of altered splice site)
460462HELIXmight get lost (downstream of altered splice site)
463473HELIXmight get lost (downstream of altered splice site)
474483STRANDmight get lost (downstream of altered splice site)
487496HELIXmight get lost (downstream of altered splice site)
497500TURNmight get lost (downstream of altered splice site)
502508STRANDmight get lost (downstream of altered splice site)
505505MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
513513BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
515517TURNmight get lost (downstream of altered splice site)
524526CONFLICTRAS -> GSA (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
534536STRANDmight get lost (downstream of altered splice site)
537541HELIXmight get lost (downstream of altered splice site)
542550STRANDmight get lost (downstream of altered splice site)
560562HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1692 / 1692
position (AA) of stopcodon in wt / mu AA sequence 564 / 564
position of stopcodon in wt / mu cDNA 1722 / 1722
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 31 / 31
chromosome 1
strand -1
last intron/exon boundary 1764
theoretical NMD boundary in CDS 1683
length of CDS 1692
coding sequence (CDS) position 1055
cDNA position
(for ins/del: last normal base / first normal base)		 1085
gDNA position
(for ins/del: last normal base / first normal base)		 25284
chromosomal position
(for ins/del: last normal base / first normal base)		 19203992
original gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
original cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
wildtype AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CSRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
mutated AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CLRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
speed 0.86 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: 0.999999999838259 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980054)
  • known disease mutation: rs4003 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:19203992G>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH4A1
Ensembl transcript ID ENST00000375341
Genbank transcript ID NM_003748
UniProt peptide P30038
alteration type single base exchange
alteration region CDS
DNA changes c.1055C>T
cDNA.1313C>T
g.25284C>T
AA changes S352L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 352
frameshift no
known variant Reference ID: rs137852937
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs4003 (pathogenic for Deficiency of pyrroline-5-carboxylate reductase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2790.964
4.9231
(flanking)4.081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased25286wt: 0.36 / mu: 0.56wt: AGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCG
mu: AGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCG		 tcgc|GTCT
Acc increased25292wt: 0.30 / mu: 0.43wt: GTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCGCTGTGG
mu: GTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCGCTGTGG		 ctct|ACGT
Donor marginally increased25289wt: 0.6604 / mu: 0.6873 (marginal change - not scored)wt: CGCGTCTCTACGTGC
mu: TGCGTCTCTACGTGC		 CGTC|tcta
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352FEYGGQKCSACSRLYVPHSLWPQI
mutated  not conserved    352FEYGGQKCSACLRLYVPHSL
Ptroglodytes  all identical  ENSPTRG00000000255  352FEYGGQKCSACSRLYVPHSL
Mmulatta  all identical  ENSMMUG00000004751  219FEYGGQKCSACSRLYVPHSLWPQ
Fcatus  all identical  ENSFCAG00000008767  351FEYGGQKCSACSRLYVPQSL
Mmusculus  all identical  ENSMUSG00000028737  351FEYGGQKCSACSRLYVPKSLW
Ggallus  all identical  ENSGALG00000003804  340FEYGGQKCSACSRLYAPRSLWPQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000038207  345FEYGGQKCSACSRMYVPDSLWPQ
Dmelanogaster  all identical  FBgn0037138  363FEYCGQKCSACSRMYVPESLWPQ
Celegans  all identical  F56D12.1  352WEYSGQKCSACSRMYAPKSIWPK
Xtropicalis  all identical  ENSXETG00000018531  326METVGQ--DGDSRARWRHRTRWR
protein features
start (aa)end (aa)featuredetails 
351357STRANDlost
352352MUTAGENS->A: Reduced affinity for NAD. No effect on enzyme activity.lost
354354CONFLICTL -> K (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
358360HELIXmight get lost (downstream of altered splice site)
361373HELIXmight get lost (downstream of altered splice site)
376376CONFLICTK -> R (in Ref. 3; BAD96206).might get lost (downstream of altered splice site)
380382TURNmight get lost (downstream of altered splice site)
394409HELIXmight get lost (downstream of altered splice site)
402402MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
413417STRANDmight get lost (downstream of altered splice site)
424426STRANDmight get lost (downstream of altered splice site)
432437STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
447447BINDINGNAD (By similarity).might get lost (downstream of altered splice site)
450458STRANDmight get lost (downstream of altered splice site)
460462HELIXmight get lost (downstream of altered splice site)
463473HELIXmight get lost (downstream of altered splice site)
474483STRANDmight get lost (downstream of altered splice site)
487496HELIXmight get lost (downstream of altered splice site)
497500TURNmight get lost (downstream of altered splice site)
502508STRANDmight get lost (downstream of altered splice site)
505505MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
513513BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
515517TURNmight get lost (downstream of altered splice site)
524526CONFLICTRAS -> GSA (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
534536STRANDmight get lost (downstream of altered splice site)
537541HELIXmight get lost (downstream of altered splice site)
542550STRANDmight get lost (downstream of altered splice site)
560562HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1692 / 1692
position (AA) of stopcodon in wt / mu AA sequence 564 / 564
position of stopcodon in wt / mu cDNA 1950 / 1950
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 259 / 259
chromosome 1
strand -1
last intron/exon boundary 1838
theoretical NMD boundary in CDS 1529
length of CDS 1692
coding sequence (CDS) position 1055
cDNA position
(for ins/del: last normal base / first normal base)		 1313
gDNA position
(for ins/del: last normal base / first normal base)		 25284
chromosomal position
(for ins/del: last normal base / first normal base)		 19203992
original gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
original cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
wildtype AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CSRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
mutated AA sequence MLLPAPALRR ALLSRPWTGA GLRWKHTSSL KVANEPVLAF TQGSPERDAL QKALKDLKGR
MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CLRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
speed 1.34 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: 0.999999999879803 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980054)
  • known disease mutation: rs4003 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:19203992G>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH4A1
Ensembl transcript ID ENST00000538309
Genbank transcript ID NM_001161504
UniProt peptide P30038
alteration type single base exchange
alteration region CDS
DNA changes c.875C>T
cDNA.1191C>T
g.25284C>T
AA changes S292L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 292
frameshift no
known variant Reference ID: rs137852937
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs4003 (pathogenic for Deficiency of pyrroline-5-carboxylate reductase) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980054)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2790.964
4.9231
(flanking)4.081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased25286wt: 0.36 / mu: 0.56wt: AGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCG
mu: AGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCG		 tcgc|GTCT
Acc increased25292wt: 0.30 / mu: 0.43wt: GTTCCGCGTGCTCGCGTCTCTACGTGCCGCACTCGCTGTGG
mu: GTTCCGCGTGCTTGCGTCTCTACGTGCCGCACTCGCTGTGG		 ctct|ACGT
Donor marginally increased25289wt: 0.6604 / mu: 0.6873 (marginal change - not scored)wt: CGCGTCTCTACGTGC
mu: TGCGTCTCTACGTGC		 CGTC|tcta
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      292FEYGGQKCSACSRLYVPHSLWPQI
mutated  not conserved    292FEYGGQKCSACLRLYVPHSL
Ptroglodytes  all identical  ENSPTRG00000000255  352FEYGGQKCSACSRLYVPHSLW
Mmulatta  all identical  ENSMMUG00000004751  219FEYGGQKCSACSRLYVPHSLWPQ
Fcatus  all identical  ENSFCAG00000008767  351FEYGGQKCSACSRLYVPQSLW
Mmusculus  all identical  ENSMUSG00000028737  351FEYGGQKCSACSRLYVPKSL
Ggallus  all identical  ENSGALG00000003804  340FEYGGQKCSACSRLYAPRSLW
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000038207  345FEYGGQKCSACSRMYVPDSLW
Dmelanogaster  all identical  FBgn0037138  363FEYCGQKCSACSRMYVPES
Celegans  all identical  F56D12.1  352WEYSGQKCSACSRMYAPKSIWPK
Xtropicalis  all identical  ENSXETG00000018531  328METVGQ--DGDSRARWRHRTR
protein features
start (aa)end (aa)featuredetails 
288300HELIXlost
302304HELIXmight get lost (downstream of altered splice site)
310314STRANDmight get lost (downstream of altered splice site)
314314ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
319323STRANDmight get lost (downstream of altered splice site)
329341HELIXmight get lost (downstream of altered splice site)
342345HELIXmight get lost (downstream of altered splice site)
348348ACT_SITENucleophile.might get lost (downstream of altered splice site)
351357STRANDmight get lost (downstream of altered splice site)
352352MUTAGENS->A: Reduced affinity for NAD. No effect on enzyme activity.might get lost (downstream of altered splice site)
354354CONFLICTL -> K (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
358360HELIXmight get lost (downstream of altered splice site)
361373HELIXmight get lost (downstream of altered splice site)
376376CONFLICTK -> R (in Ref. 3; BAD96206).might get lost (downstream of altered splice site)
380382TURNmight get lost (downstream of altered splice site)
394409HELIXmight get lost (downstream of altered splice site)
402402MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
413417STRANDmight get lost (downstream of altered splice site)
424426STRANDmight get lost (downstream of altered splice site)
432437STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
447447BINDINGNAD (By similarity).might get lost (downstream of altered splice site)
450458STRANDmight get lost (downstream of altered splice site)
460462HELIXmight get lost (downstream of altered splice site)
463473HELIXmight get lost (downstream of altered splice site)
474483STRANDmight get lost (downstream of altered splice site)
487496HELIXmight get lost (downstream of altered splice site)
497500TURNmight get lost (downstream of altered splice site)
502508STRANDmight get lost (downstream of altered splice site)
505505MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
513513BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
515517TURNmight get lost (downstream of altered splice site)
524526CONFLICTRAS -> GSA (in Ref. 9; AA sequence).might get lost (downstream of altered splice site)
534536STRANDmight get lost (downstream of altered splice site)
537541HELIXmight get lost (downstream of altered splice site)
542550STRANDmight get lost (downstream of altered splice site)
560562HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1512 / 1512
position (AA) of stopcodon in wt / mu AA sequence 504 / 504
position of stopcodon in wt / mu cDNA 1828 / 1828
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 317 / 317
chromosome 1
strand -1
last intron/exon boundary 1716
theoretical NMD boundary in CDS 1349
length of CDS 1512
coding sequence (CDS) position 875
cDNA position
(for ins/del: last normal base / first normal base)		 1191
gDNA position
(for ins/del: last normal base / first normal base)		 25284
chromosomal position
(for ins/del: last normal base / first normal base)		 19203992
original gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered gDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
original cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTCGCGTCTCTACGTGCCGCACT
altered cDNA sequence snippet CCAGAAGTGTTCCGCGTGCTTGCGTCTCTACGTGCCGCACT
wildtype AA sequence MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CSRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
mutated AA sequence MEAIPCVVGD EEVWTSDVQY QVSPFNHGHK VAKFCYADKS LLNKAIEAAL AARKEWDLKP
IADRAQIFLK AADMLSGPRR AEILAKTMVG QGKTVIQAEI DAAAELIDFF RFNAKYAVEL
EGQQPISVPP STNSTVYRGL EGFVAAISPF NFTAIGGNLA GAPALMGNVV LWKPSDTAML
ASYAVYRILR EAGLPPNIIQ FVPADGPLFG DTVTSSEHLC GINFTGSVPT FKHLWKQVAQ
NLDRFHTFPR LAGECGGKNF HFVHRSADVE SVVSGTLRSA FEYGGQKCSA CLRLYVPHSL
WPQIKGRLLE EHSRIKVGDP AEDFGTFFSA VIDAKSFARI KKWLEHARSS PSLTILAGGK
CDDSVGYFVE PCIVESKDPQ EPIMKEEIFG PVLSVYVYPD DKYKETLQLV DSTTSYGLTG
AVFSQDKDVV QEATKVLRNA AGNFYINDKS TGSIVGQQPF GGARASGTND KPGGPHYILR
WTSPQVIKET HKPLGDWSYA YMQ*
speed 0.50 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