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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000407721
Querying Taster for transcript #2: ENST00000355527
MT speed 0 s - this script 3.2481 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DHCR7disease_causing0.999999997005724simple_aaeaffectedM59Rsingle base exchangers104886036show file
DHCR7disease_causing0.999999997005724simple_aaeaffectedM59Rsingle base exchangers104886036show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997005724      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM004034)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:71155184A>CN/A show variant in all transcripts   IGV
HGNC symbol DHCR7
Ensembl transcript ID ENST00000407721
Genbank transcript ID N/A
UniProt peptide Q9UBM7
alteration type single base exchange
alteration region CDS
DNA changes c.176T>G
cDNA.388T>G
g.8731T>G
AA changes M59R Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 59
frameshift no
known variant Reference ID: rs104886036
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6981
3.8931
(flanking)3.8931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8730wt: 0.47 / mu: 0.92wt: TCATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGC
mu: TCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGC		 atca|TGGC
Acc increased8723wt: 0.30 / mu: 0.55wt: GCCCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCA
mu: GCCCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCA		 ctac|TTCA
Acc increased8727wt: 0.30 / mu: 0.38wt: CCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGTAC
mu: CCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTAC		 ttca|TCAT
Acc marginally increased8722wt: 0.9600 / mu: 0.9650 (marginal change - not scored)wt: CGCCCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACC
mu: CGCCCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACC		 acta|CTTC
Acc marginally increased8726wt: 0.8763 / mu: 0.8973 (marginal change - not scored)wt: CCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGTA
mu: CCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTA		 cttc|ATCA
Acc marginally increased8725wt: 0.8845 / mu: 0.9180 (marginal change - not scored)wt: CCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGT
mu: CCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGT		 actt|CATC
Donor gained87310.33mu: CATCAGGGCTTGTGA TCAG|ggct
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      59LFAPFIVYYFIMACDQYSCALTGP
mutated  not conserved    59LFAPFIVYYFIRACDQYSCALTG
Ptroglodytes  all identical  ENSPTRG00000004013  59LFAPFIVYYFIMACDQYSCALTG
Mmulatta  all identical  ENSMMUG00000011976  59LCAPFIVYYFIMACDQYSCALTG
Fcatus  all identical  ENSFCAG00000004115  59LLAPFIVYYFIMACDQYGCSLTA
Mmusculus  all identical  ENSMUSG00000058454  59LFAPFIVYYFIMACDQYSCSLTA
Ggallus  all identical  ENSGALG00000004106  59AFAPLIVYYFIMSCDQYQCSLTD
Trubripes  all identical  ENSTRUG00000003928  59CFAPFIVFYFVMACDQHQCSLSQ
Drerio  all identical  ENSDARG00000015564  62CFAPFLVFFFIMACDQYQCSISH
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008945  57AFAPLIVYYFVMSCDQYQCALTA
protein features
start (aa)end (aa)featuredetails 
4060TRANSMEMHelical; (Potential).lost
154174TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
177197TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
266286TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
306326TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
331351TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
420440TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1428 / 1428
position (AA) of stopcodon in wt / mu AA sequence 476 / 476
position of stopcodon in wt / mu cDNA 1640 / 1640
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 213 / 213
chromosome 11
strand -1
last intron/exon boundary 1176
theoretical NMD boundary in CDS 913
length of CDS 1428
coding sequence (CDS) position 176
cDNA position
(for ins/del: last normal base / first normal base)		 388
gDNA position
(for ins/del: last normal base / first normal base)		 8731
chromosomal position
(for ins/del: last normal base / first normal base)		 71155184
original gDNA sequence snippet CATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGCT
altered gDNA sequence snippet CATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGCT
original cDNA sequence snippet CATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGCT
altered cDNA sequence snippet CATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGCT
wildtype AA sequence MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIMA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNETW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*
mutated AA sequence MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIRA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNETW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*
speed 0.34 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997005724      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM004034)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:71155184A>CN/A show variant in all transcripts   IGV
HGNC symbol DHCR7
Ensembl transcript ID ENST00000355527
Genbank transcript ID NM_001163817
UniProt peptide Q9UBM7
alteration type single base exchange
alteration region CDS
DNA changes c.176T>G
cDNA.453T>G
g.8731T>G
AA changes M59R Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 59
frameshift no
known variant Reference ID: rs104886036
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004034)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6981
3.8931
(flanking)3.8931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8730wt: 0.47 / mu: 0.92wt: TCATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGC
mu: TCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGC		 atca|TGGC
Acc increased8723wt: 0.30 / mu: 0.55wt: GCCCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCA
mu: GCCCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCA		 ctac|TTCA
Acc increased8727wt: 0.30 / mu: 0.38wt: CCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGTAC
mu: CCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTAC		 ttca|TCAT
Acc marginally increased8722wt: 0.9600 / mu: 0.9650 (marginal change - not scored)wt: CGCCCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACC
mu: CGCCCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACC		 acta|CTTC
Acc marginally increased8726wt: 0.8763 / mu: 0.8973 (marginal change - not scored)wt: CCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGTA
mu: CCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGTA		 cttc|ATCA
Acc marginally increased8725wt: 0.8845 / mu: 0.9180 (marginal change - not scored)wt: CCCCTTCATCGTCTACTACTTCATCATGGCTTGTGACCAGT
mu: CCCCTTCATCGTCTACTACTTCATCAGGGCTTGTGACCAGT		 actt|CATC
Donor gained87310.33mu: CATCAGGGCTTGTGA TCAG|ggct
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      59LFAPFIVYYFIMACDQYSCALTGP
mutated  not conserved    59LFAPFIVYYFIRACDQYSCALTG
Ptroglodytes  all identical  ENSPTRG00000004013  59LFAPFIVYYFIMACDQYSCALTG
Mmulatta  all identical  ENSMMUG00000011976  59LCAPFIVYYFIMACDQYSCALTG
Fcatus  all identical  ENSFCAG00000004115  59LLAPFIVYYFIMACDQYGCSLTA
Mmusculus  all identical  ENSMUSG00000058454  59LFAPFIVYYFIMACDQYSCSLTA
Ggallus  all identical  ENSGALG00000004106  59AFAPLIVYYFIMSCDQYQCSLTD
Trubripes  all identical  ENSTRUG00000003928  59CFAPFIVFYFVMACDQHQCSLSQ
Drerio  all identical  ENSDARG00000015564  62CFAPFLVFFFIMACDQYQCSISH
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008945  57AFAPLIVYYFVMSCDQYQCALTA
protein features
start (aa)end (aa)featuredetails 
4060TRANSMEMHelical; (Potential).lost
154174TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
177197TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
266286TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
306326TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
331351TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
420440TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1428 / 1428
position (AA) of stopcodon in wt / mu AA sequence 476 / 476
position of stopcodon in wt / mu cDNA 1705 / 1705
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 278 / 278
chromosome 11
strand -1
last intron/exon boundary 1241
theoretical NMD boundary in CDS 913
length of CDS 1428
coding sequence (CDS) position 176
cDNA position
(for ins/del: last normal base / first normal base)		 453
gDNA position
(for ins/del: last normal base / first normal base)		 8731
chromosomal position
(for ins/del: last normal base / first normal base)		 71155184
original gDNA sequence snippet CATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGCT
altered gDNA sequence snippet CATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGCT
original cDNA sequence snippet CATCGTCTACTACTTCATCATGGCTTGTGACCAGTACAGCT
altered cDNA sequence snippet CATCGTCTACTACTTCATCAGGGCTTGTGACCAGTACAGCT
wildtype AA sequence MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIMA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNETW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*
mutated AA sequence MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIRA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNETW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*
speed 0.91 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