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 10 transcript(s)...
Querying Taster for transcript #1: ENST00000361732
Querying Taster for transcript #2: ENST00000509734
Querying Taster for transcript #3: ENST00000354868
Querying Taster for transcript #4: ENST00000521422
Querying Taster for transcript #5: ENST00000354312
Querying Taster for transcript #6: ENST00000345306
Querying Taster for transcript #7: ENST00000305138
Querying Taster for transcript #8: ENST00000282891
Querying Taster for transcript #9: ENST00000380774
Querying Taster for transcript #10: ENST00000358030
MT speed 0 s - this script 8.80199 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
RAD17polymorphism_automatic0.999999904277265simple_aaeaffectedL381Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999904277265simple_aaeaffectedL381Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL546Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL557Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL546Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL546Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL546Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL546Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL460Rsingle base exchangers1045051show file
RAD17polymorphism_automatic0.999999926484947simple_aaeaffectedL557Rsingle base exchangers1045051show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 9.57227350036922e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000521422
Genbank transcript ID N/A
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1142T>G
cDNA.1879T>G
g.30821T>G
AA changes L381R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 381
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      381LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    381LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.might get lost (downstream of altered splice site)
445445CONFLICTP -> S (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
462462CONFLICTM -> T (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1518 / 1518
position (AA) of stopcodon in wt / mu AA sequence 506 / 506
position of stopcodon in wt / mu cDNA 2255 / 2255
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 738 / 738
chromosome 5
strand 1
last intron/exon boundary 1994
theoretical NMD boundary in CDS 1206
length of CDS 1518
coding sequence (CDS) position 1142
cDNA position
(for ins/del: last normal base / first normal base)		 1879
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC LQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
mutated AA sequence MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC RQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
speed 0.97 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

polymorphism

 Model: simple_aae, prob: 9.57227350036922e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000358030
Genbank transcript ID NM_133340
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1142T>G
cDNA.1765T>G
g.30821T>G
AA changes L381R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 381
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      381LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    381LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.might get lost (downstream of altered splice site)
445445CONFLICTP -> S (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
462462CONFLICTM -> T (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1518 / 1518
position (AA) of stopcodon in wt / mu AA sequence 506 / 506
position of stopcodon in wt / mu cDNA 2141 / 2141
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 624 / 624
chromosome 5
strand 1
last intron/exon boundary 1880
theoretical NMD boundary in CDS 1206
length of CDS 1518
coding sequence (CDS) position 1142
cDNA position
(for ins/del: last normal base / first normal base)		 1765
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC LQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
mutated AA sequence MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC RQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
speed 1.21 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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000361732
Genbank transcript ID NM_133343
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.2117T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2493 / 2493
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 481 / 481
chromosome 5
strand 1
last intron/exon boundary 2232
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 2117
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
speed 1.17 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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000509734
Genbank transcript ID NM_133339
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1670T>G
cDNA.2348T>G
g.30821T>G
AA changes L557R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 557
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      557LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    557LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2046 / 2046
position (AA) of stopcodon in wt / mu AA sequence 682 / 682
position of stopcodon in wt / mu cDNA 2724 / 2724
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 679 / 679
chromosome 5
strand 1
last intron/exon boundary 2463
theoretical NMD boundary in CDS 1734
length of CDS 2046
coding sequence (CDS) position 1670
cDNA position
(for ins/del: last normal base / first normal base)		 2348
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCLQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
mutated AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCRQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000354868
Genbank transcript ID NM_133338
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.2175T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2551 / 2551
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 539 / 539
chromosome 5
strand 1
last intron/exon boundary 2290
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 2175
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000354312
Genbank transcript ID NM_133342
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.2058T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2434 / 2434
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 422 / 422
chromosome 5
strand 1
last intron/exon boundary 2173
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 2058
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
speed 1.38 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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000345306
Genbank transcript ID NM_133344
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.1904T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2280 / 2280
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 268 / 268
chromosome 5
strand 1
last intron/exon boundary 2019
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 1904
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
speed 1.01 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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000305138
Genbank transcript ID NM_002873
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.2279T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2655 / 2655
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 643 / 643
chromosome 5
strand 1
last intron/exon boundary 2394
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 2279
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
speed 1.45 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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000282891
Genbank transcript ID NM_133341
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1379T>G
cDNA.1691T>G
g.30821T>G
AA changes L460R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 460
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      460LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    460LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  569LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  538LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  548LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  557LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
462462CONFLICTM -> T (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1755 / 1755
position (AA) of stopcodon in wt / mu AA sequence 585 / 585
position of stopcodon in wt / mu cDNA 2067 / 2067
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 313 / 313
chromosome 5
strand 1
last intron/exon boundary 1806
theoretical NMD boundary in CDS 1443
length of CDS 1755
coding sequence (CDS) position 1379
cDNA position
(for ins/del: last normal base / first normal base)		 1691
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MNQHELAVHK KKIEEVETWL KAQVLERQPK QGGSILLITG PPGCGKTTTL KILSKEHGIQ
VQEWINPVLP DFQKDDFKGM FNTESSFHMF PYQSQIAVFK EFLLRATKYN KLQMLGDDLR
TDKKIILVED LPNQFYRDSH TLHEVLRKYV RIGRCPLIFI ISDSLSGDNN QRLLFPKEIQ
EECSISNISF NPVAPTIMMK FLNRIVTIEA NKNGGKITVP DKTSLELLCQ GCSGDIRSAI
NSLQFSSSKG ENNLRPRKKG MSLKSDAVLS KSKRRKKPDR VFENQEVQAI GGKDVSLFLF
RALGKILYCK RASLTELDSP RLPSHLSEYE RDTLLVEPEE VVEMSHMPGD LFNLYLHQNY
IDFFMEIDDI VRASEFLSFA DILSGDWNTR SLLREYSTSI ATRGVMHSNK ARGYAHCQGG
GSSFRPLHKP QWFLINKKYR ENCLAAKALF PDFCLPALCL QTQLLPYLAL LTIPMRNQAQ
ISFIQDIGRL PLKRHFGRLK MEALTDREHG MIDPDSGDEA QLNGGHSAEE SLGEPTQATV
PETWSLPLSQ NSASELPASQ PQPFSAQGDM EENIIIEDYE SDGT*
mutated AA sequence MNQHELAVHK KKIEEVETWL KAQVLERQPK QGGSILLITG PPGCGKTTTL KILSKEHGIQ
VQEWINPVLP DFQKDDFKGM FNTESSFHMF PYQSQIAVFK EFLLRATKYN KLQMLGDDLR
TDKKIILVED LPNQFYRDSH TLHEVLRKYV RIGRCPLIFI ISDSLSGDNN QRLLFPKEIQ
EECSISNISF NPVAPTIMMK FLNRIVTIEA NKNGGKITVP DKTSLELLCQ GCSGDIRSAI
NSLQFSSSKG ENNLRPRKKG MSLKSDAVLS KSKRRKKPDR VFENQEVQAI GGKDVSLFLF
RALGKILYCK RASLTELDSP RLPSHLSEYE RDTLLVEPEE VVEMSHMPGD LFNLYLHQNY
IDFFMEIDDI VRASEFLSFA DILSGDWNTR SLLREYSTSI ATRGVMHSNK ARGYAHCQGG
GSSFRPLHKP QWFLINKKYR ENCLAAKALF PDFCLPALCR QTQLLPYLAL LTIPMRNQAQ
ISFIQDIGRL PLKRHFGRLK MEALTDREHG MIDPDSGDEA QLNGGHSAEE SLGEPTQATV
PETWSLPLSQ NSASELPASQ PQPFSAQGDM EENIIIEDYE SDGT*
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

polymorphism

 Model: simple_aae, prob: 7.35150531844382e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000380774
Genbank transcript ID N/A
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1670T>G
cDNA.1732T>G
g.30821T>G
AA changes L557R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 557
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      557LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    557LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2046 / 2046
position (AA) of stopcodon in wt / mu AA sequence 682 / 682
position of stopcodon in wt / mu cDNA 2108 / 2108
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 63 / 63
chromosome 5
strand 1
last intron/exon boundary 1847
theoretical NMD boundary in CDS 1734
length of CDS 2046
coding sequence (CDS) position 1670
cDNA position
(for ins/del: last normal base / first normal base)		 1732
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCLQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
mutated AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCRQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
speed 1.26 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