Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000444495
Querying Taster for transcript #2: ENST00000397676
Querying Taster for transcript #3: ENST00000445626
Querying Taster for transcript #4: ENST00000455059
Querying Taster for transcript #5: ENST00000418734
MT speed 0 s - this script 6.343008 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALG3disease_causing_automatic0.999999984857781simple_aaeaffected0W71Rsingle base exchangers119103237show file
ALG3disease_causing_automatic0.999999984857781simple_aaeaffected0W23Rsingle base exchangers119103237show file
ALG3disease_causing_automatic0.999999984857781simple_aaeaffected0W31Rsingle base exchangers119103237show file
EIF2B5disease_causing_automatic1without_aaeaffected0single base exchangers119103237show file
ALG3disease_causing_automatic1without_aaeaffected0single base exchangers119103237show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999984857781 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/A show variant in all transcripts   IGV
HGNC symbol ALG3
Ensembl transcript ID ENST00000397676
Genbank transcript ID NM_005787
UniProt peptide Q92685
alteration type single base exchange
alteration region CDS
DNA changes c.211T>C
cDNA.242T>C
g.3751T>C
AA changes W71R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
frameshift no
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased3742wt: 0.3767 / mu: 0.4272 (marginal change - not scored)wt: CTTGTCTTCTTCCAGACACAGAGATTGACTGGAAGGCCTAC
mu: CTTGTCTTCTTCCAGACACAGAGATTGACCGGAAGGCCTAC		 acag|AGAT
Donor marginally increased3751wt: 0.9050 / mu: 0.9580 (marginal change - not scored)wt: TTGACTGGAAGGCCT
mu: TTGACCGGAAGGCCT		 GACT|ggaa
Donor increased3750wt: 0.81 / mu: 0.97wt: ATTGACTGGAAGGCC
mu: ATTGACCGGAAGGCC		 TGAC|tgga
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71VIHRVAYTEIDWKAYMAEVEGVIN
mutated  not conserved    71IHRVAYTEIDRKAYMAEVEGVI
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000018951  n/a
Fcatus  all identical  ENSFCAG00000016274  71IHRVAYTEIDWKAYMAQVEGVI
Mmusculus  all identical  ENSMUSG00000033809  71IHRVAYTEIDWKAYMAQVEGFI
Ggallus  all identical  ENSGALG00000008503  9RPADTEIDWQAYMQEVEGFA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000053155  65IQKVSYTEIDWKAYMDEVEGVI
Dmelanogaster  all identical  FBgn0011297  74VIQRVPYTEIDWVAYMQECEGFL
Celegans  all identical  K09E4.2  49VILKVNYTEIDWSTYMQQVECYV
Xtropicalis  all identical  ENSXETG00000017280  73QRVPYTEIDWKAYMDEVEGVL
protein features
start (aa)end (aa)featuredetails 
95115TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123143TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
149169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
172192TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
203223TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
289309TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332352TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
356376TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1317 / 1317
position (AA) of stopcodon in wt / mu AA sequence 439 / 439
position of stopcodon in wt / mu cDNA 1348 / 1348
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 32 / 32
chromosome 3
strand -1
last intron/exon boundary 1186
theoretical NMD boundary in CDS 1104
length of CDS 1317
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)		 242
gDNA position
(for ins/del: last normal base / first normal base)		 3751
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet TTCCAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered gDNA sequence snippet TTCCAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
original cDNA sequence snippet TGGCATACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered cDNA sequence snippet TGGCATACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
wildtype AA sequence MAAGLRKRGR SGSAAQAEGL CKQWLQRAWQ ERRLLLREPR YTLLVAACLC LAEVGITFWV
IHRVAYTEID WKAYMAEVEG VINGTYDYTQ LQGDTGPLVY PAGFVYIFMG LYYATSRGTD
IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA SYRVHSIFVL RLFNDPVAMV
LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF LLLTQFGFRG ALPKLGICAG
LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP EALFLHRAFH LALLTAHLTL
LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS TLFTSNFIGI CFSRSLHYQF
YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP STSCSSAALH ICHAVILLQL
WLGPQPFPKS TQHSKKAH*
mutated AA sequence MAAGLRKRGR SGSAAQAEGL CKQWLQRAWQ ERRLLLREPR YTLLVAACLC LAEVGITFWV
IHRVAYTEID RKAYMAEVEG VINGTYDYTQ LQGDTGPLVY PAGFVYIFMG LYYATSRGTD
IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA SYRVHSIFVL RLFNDPVAMV
LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF LLLTQFGFRG ALPKLGICAG
LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP EALFLHRAFH LALLTAHLTL
LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS TLFTSNFIGI CFSRSLHYQF
YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP STSCSSAALH ICHAVILLQL
WLGPQPFPKS TQHSKKAH*
speed 1.37 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: 0.999999984857781 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/A show variant in all transcripts   IGV
HGNC symbol ALG3
Ensembl transcript ID ENST00000445626
Genbank transcript ID NM_001006941
UniProt peptide Q92685
alteration type single base exchange
alteration region CDS
DNA changes c.67T>C
cDNA.338T>C
g.3751T>C
AA changes W23R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 23
frameshift no
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased3742wt: 0.3767 / mu: 0.4272 (marginal change - not scored)wt: CTTGTCTTCTTCCAGACACAGAGATTGACTGGAAGGCCTAC
mu: CTTGTCTTCTTCCAGACACAGAGATTGACCGGAAGGCCTAC		 acag|AGAT
Donor marginally increased3751wt: 0.9050 / mu: 0.9580 (marginal change - not scored)wt: TTGACTGGAAGGCCT
mu: TTGACCGGAAGGCCT		 GACT|ggaa
Donor increased3750wt: 0.81 / mu: 0.97wt: ATTGACTGGAAGGCC
mu: ATTGACCGGAAGGCC		 TGAC|tgga
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      23FSGCGGDTEIDWKAYMAEVEGVIN
mutated  not conserved    23FSGCGGDTEIDRKAYMAEVEGVI
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000018951  n/a
Fcatus  all identical  ENSFCAG00000016274  71TEIDWKAYMAQVEGVI
Mmusculus  all identical  ENSMUSG00000033809  71TEIDWKAYMAQVEGFI
Ggallus  all identical  ENSGALG00000008503  9DTEIDWQAYMQEVEGFA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000053155  65TEIDWKAYMDEVEGVI
Dmelanogaster  all identical  FBgn0011297  74TEIDWVAYMQECEGFL
Celegans  all identical  K09E4.2  49TEIDWSTYMQQVECYV
Xtropicalis  all identical  ENSXETG00000017280  73TEIDWKAYMDEVEGVL
protein features
start (aa)end (aa)featuredetails 
4161TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
95115TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123143TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
149169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
172192TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
203223TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
289309TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332352TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
356376TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1173 / 1173
position (AA) of stopcodon in wt / mu AA sequence 391 / 391
position of stopcodon in wt / mu cDNA 1444 / 1444
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 272 / 272
chromosome 3
strand -1
last intron/exon boundary 1282
theoretical NMD boundary in CDS 960
length of CDS 1173
coding sequence (CDS) position 67
cDNA position
(for ins/del: last normal base / first normal base)		 338
gDNA position
(for ins/del: last normal base / first normal base)		 3751
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet TTCCAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered gDNA sequence snippet TTCCAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
original cDNA sequence snippet GGGGAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered cDNA sequence snippet GGGGAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
wildtype AA sequence MFPAQAKENA GFSGCGGDTE IDWKAYMAEV EGVINGTYDY TQLQGDTGPL VYPAGFVYIF
MGLYYATSRG TDIRMAQNIF AVLYLATLLL VFLIYHQTCK VPPFVFFFMC CASYRVHSIF
VLRLFNDPVA MVLLFLSINL LLAQRWGWGC CFFSLAVSVK MNVLLFAPGL LFLLLTQFGF
RGALPKLGIC AGLQVVLGLP FLLENPSGYL SRSFDLGRQF LFHWTVNWRF LPEALFLHRA
FHLALLTAHL TLLLLFALCR WHRTGESILS LLRDPSKRKV PPQPLTPNQI VSTLFTSNFI
GICFSRSLHY QFYVWYFHTL PYLLWAMPAR WLTHLLRLLV LGLIELSWNT YPSTSCSSAA
LHICHAVILL QLWLGPQPFP KSTQHSKKAH *
mutated AA sequence MFPAQAKENA GFSGCGGDTE IDRKAYMAEV EGVINGTYDY TQLQGDTGPL VYPAGFVYIF
MGLYYATSRG TDIRMAQNIF AVLYLATLLL VFLIYHQTCK VPPFVFFFMC CASYRVHSIF
VLRLFNDPVA MVLLFLSINL LLAQRWGWGC CFFSLAVSVK MNVLLFAPGL LFLLLTQFGF
RGALPKLGIC AGLQVVLGLP FLLENPSGYL SRSFDLGRQF LFHWTVNWRF LPEALFLHRA
FHLALLTAHL TLLLLFALCR WHRTGESILS LLRDPSKRKV PPQPLTPNQI VSTLFTSNFI
GICFSRSLHY QFYVWYFHTL PYLLWAMPAR WLTHLLRLLV LGLIELSWNT YPSTSCSSAA
LHICHAVILL QLWLGPQPFP KSTQHSKKAH *
speed 1.15 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: 0.999999984857781 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/A show variant in all transcripts   IGV
HGNC symbol ALG3
Ensembl transcript ID ENST00000455059
Genbank transcript ID N/A
UniProt peptide Q92685
alteration type single base exchange
alteration region CDS
DNA changes c.91T>C
cDNA.546T>C
g.3751T>C
AA changes W31R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 31
frameshift no
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased3742wt: 0.3767 / mu: 0.4272 (marginal change - not scored)wt: CTTGTCTTCTTCCAGACACAGAGATTGACTGGAAGGCCTAC
mu: CTTGTCTTCTTCCAGACACAGAGATTGACCGGAAGGCCTAC		 acag|AGAT
Donor marginally increased3751wt: 0.9050 / mu: 0.9580 (marginal change - not scored)wt: TTGACTGGAAGGCCT
mu: TTGACCGGAAGGCCT		 GACT|ggaa
Donor increased3750wt: 0.81 / mu: 0.97wt: ATTGACTGGAAGGCC
mu: ATTGACCGGAAGGCC		 TGAC|tgga
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      31RNLSVEDTEIDWKAYMAEVEGVIN
mutated  not conserved    31RNLSVEDTEIDRKAYMAEVEGVI
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000018951  n/a
Fcatus  all identical  ENSFCAG00000016274  71TEIDWKAYMAQVEGVI
Mmusculus  all identical  ENSMUSG00000033809  71TEIDWKAYMAQVEGFI
Ggallus  all identical  ENSGALG00000008503  9DTEIDWQAYMQEVEGFA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000053155  65VSYTEIDWKAYMDEVEGVI
Dmelanogaster  all identical  FBgn0011297  74TEIDWVAYMQECEGFL
Celegans  all identical  K09E4.2  49LKVNYTEIDWSTYMQQVECYV
Xtropicalis  all identical  ENSXETG00000017280  73TEIDWKAYMDEVEGVL
protein features
start (aa)end (aa)featuredetails 
4161TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
95115TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123143TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
149169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
172192TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
203223TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
289309TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332352TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
356376TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1197 / 1197
position (AA) of stopcodon in wt / mu AA sequence 399 / 399
position of stopcodon in wt / mu cDNA 1652 / 1652
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 456 / 456
chromosome 3
strand -1
last intron/exon boundary 1490
theoretical NMD boundary in CDS 984
length of CDS 1197
coding sequence (CDS) position 91
cDNA position
(for ins/del: last normal base / first normal base)		 546
gDNA position
(for ins/del: last normal base / first normal base)		 3751
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet TTCCAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered gDNA sequence snippet TTCCAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
original cDNA sequence snippet TCGAAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered cDNA sequence snippet TCGAAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
wildtype AA sequence MKTGYSDRRL AWWDARHGKR NLSVEDTEID WKAYMAEVEG VINGTYDYTQ LQGDTGPLVY
PAGFVYIFMG LYYATSRGTD IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA
SYRVHSIFVL RLFNDPVAMV LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF
LLLTQFGFRG ALPKLGICAG LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP
EALFLHRAFH LALLTAHLTL LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS
TLFTSNFIGI CFSRSLHYQF YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP
STSCSSAALH ICHAVILLQL WLGPQPFPKS TQHSKKAH*
mutated AA sequence MKTGYSDRRL AWWDARHGKR NLSVEDTEID RKAYMAEVEG VINGTYDYTQ LQGDTGPLVY
PAGFVYIFMG LYYATSRGTD IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA
SYRVHSIFVL RLFNDPVAMV LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF
LLLTQFGFRG ALPKLGICAG LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP
EALFLHRAFH LALLTAHLTL LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS
TLFTSNFIGI CFSRSLHYQF YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP
STSCSSAALH ICHAVILLQL WLGPQPFPKS TQHSKKAH*
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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/A show variant in all transcripts   IGV
HGNC symbol EIF2B5
Ensembl transcript ID ENST00000444495
Genbank transcript ID N/A
UniProt peptide Q13144
alteration type single base exchange
alteration region intron
DNA changes g.110761A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased110771wt: 0.38 / mu: 0.53wt: TAGGCCTTCCAGTCAATCTCTGTGTCTGGAAGAAGACAAGA
mu: TAGGCCTTCCGGTCAATCTCTGTGTCTGGAAGAAGACAAGA		 ctct|GTGT
Acc marginally increased110751wt: 0.7591 / mu: 0.8285 (marginal change - not scored)wt: CGCCTTCTACCTCGGCCATGTAGGCCTTCCAGTCAATCTCT
mu: CGCCTTCTACCTCGGCCATGTAGGCCTTCCGGTCAATCTCT		 atgt|AGGC
Acc increased110753wt: 0.25 / mu: 0.45wt: CCTTCTACCTCGGCCATGTAGGCCTTCCAGTCAATCTCTGT
mu: CCTTCTACCTCGGCCATGTAGGCCTTCCGGTCAATCTCTGT		 gtag|GCCT
distance from splice site 99999
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
543720DOMAINW2.might get lost (downstream of altered splice site)
701714HELIXmight get lost (downstream of altered splice site)
717717MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
718718MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 11 / 11
chromosome 3
strand 1
last intron/exon boundary 2117
theoretical NMD boundary in CDS 2056
length of CDS 2118
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 110761
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet CTCGGCCATGTAGGCCTTCCAGTCAATCTCTGTGTCTGGAA
altered gDNA sequence snippet CTCGGCCATGTAGGCCTTCCGGTCAATCTCTGTGTCTGGAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLLKSK WCRPTSLNVV
RIITSELYRS LGDVLRDVDA KALVRSDFLL VYGDVISNIN ITRALEEHRL RRKLEKNVSV
MTMIFKESSP SHPTRCHEDN VVVAVDSTTN RVLHFQKTQG LRRFAFPLSL FQGSSDGVEV
RYDLLDCHIS ICSPQVAQLF TDNFDYQTRD DFVRGLLVNE EILGNQIHMH VTAKEYGARV
SNLHMYSAVC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQVVC*
mutated AA sequence N/A
speed 0.99 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/A show variant in all transcripts   IGV
HGNC symbol ALG3
Ensembl transcript ID ENST00000418734
Genbank transcript ID N/A
UniProt peptide Q92685
alteration type single base exchange
alteration region intron
DNA changes g.3751T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased3742wt: 0.3767 / mu: 0.4272 (marginal change - not scored)wt: CTTGTCTTCTTCCAGACACAGAGATTGACTGGAAGGCCTAC
mu: CTTGTCTTCTTCCAGACACAGAGATTGACCGGAAGGCCTAC		 acag|AGAT
Donor marginally increased3751wt: 0.9050 / mu: 0.9580 (marginal change - not scored)wt: TTGACTGGAAGGCCT
mu: TTGACCGGAAGGCCT		 GACT|ggaa
Donor increased3750wt: 0.81 / mu: 0.97wt: ATTGACTGGAAGGCC
mu: ATTGACCGGAAGGCC		 TGAC|tgga
distance from splice site 183
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
4161TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
95115TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123143TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
149169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
172192TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
203223TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
289309TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332352TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
356376TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 91 / 91
chromosome 3
strand -1
last intron/exon boundary 1077
theoretical NMD boundary in CDS 936
length of CDS 1149
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 3751
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet TTCCAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered gDNA sequence snippet TTCCAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAAARLARAA PAAAGAALHA AGGRLPLPGG GGHHLLGHSQ GGMYPAGFVY IFMGLYYATS
RGTDIRMAQN IFAVLYLATL LLVFLIYHQT CKVPPFVFFF MCCASYRVHS IFVLRLFNDP
VAMVLLFLSI NLLLAQRWGW GCCFFSLAVS VKMNVLLFAP GLLFLLLTQF GFRGALPKLG
ICAGLQVVLG LPFLLENPSG YLSRSFDLGR QFLFHWTVNW RFLPEALFLH RAFHLALLTA
HLTLLLLFAL CRWHRTGESI LSLLRDPSKR KVPPQPLTPN QIVSTLFTSN FIGICFSRSL
HYQFYVWYFH TLPYLLWAMP ARWLTHLLRL LVLGLIELSW NTYPSTSCSS AALHICHAVI
LLQLWLGPQP FPKSTQHSKK AH*
mutated AA sequence N/A
speed 0.99 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