Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000295171
Querying Taster for transcript #2: ENST00000409856
Querying Taster for transcript #3: ENST00000434330
Querying Taster for transcript #4: ENST00000467992
MT speed 3.98 s - this script 6.480173 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CCDC74Apolymorphism_automatic3.99680288865056e-15simple_aaeaffectedM169Tsingle base exchangers201632382show file
CCDC74Apolymorphism_automatic3.99680288865056e-15simple_aaeaffectedM271Tsingle base exchangers201632382show file
CCDC74Apolymorphism_automatic3.99680288865056e-15simple_aaeaffectedM103Tsingle base exchangers201632382show file

some transcripts had annotation problems and are not shown

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999996 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:132288362T>CN/A show variant in all transcripts   IGV
HGNC symbol CCDC74A
Ensembl transcript ID ENST00000295171
Genbank transcript ID NM_138770
UniProt peptide Q96LY2
alteration type single base exchange
alteration region CDS
DNA changes c.506T>C
cDNA.644T>C
g.3115T>C
AA changes M169T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
169
frameshift no
known variant Reference ID: rs201632382
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC48171723122048
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.410.004
-0.5290.001
(flanking)-1.8630
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 increased3115wt: 0.2715 / mu: 0.2836 (marginal change - not scored)wt: TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
mu: TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
 ccat|GTCA
Donor increased3110wt: 0.58 / mu: 0.76wt: AGCCTCTCCATGTCA
mu: AGCCTCTCCACGTCA
 CCTC|tcca
Donor marginally increased3115wt: 0.9978 / mu: 0.9983 (marginal change - not scored)wt: CTCCATGTCAAGCTT
mu: CTCCACGTCAAGCTT
 CCAT|gtca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      169DTVRSPADSLSMSSFQSVKSISNS
mutated  not conserved    169DTVRSPADSLSTSSFQSVKSISN
Ptroglodytes  not conserved  ENSPTRG00000012471  169DTVRSPADSLSTSSFQSVKSISN
Mmulatta  not conserved  ENSMMUG00000003066  266-LRSPADSLSTSSFPSVKSISN
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000041617  144HSGKSASNS--------TMS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000093026  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1137 / 1137
position (AA) of stopcodon in wt / mu AA sequence 379 / 379
position of stopcodon in wt / mu cDNA 1275 / 1275
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 139 / 139
chromosome 2
strand 1
last intron/exon boundary 1146
theoretical NMD boundary in CDS 957
length of CDS 1137
coding sequence (CDS) position 506
cDNA position
(for ins/del: last normal base / first normal base)
644
gDNA position
(for ins/del: last normal base / first normal base)
3115
chromosomal position
(for ins/del: last normal base / first normal base)
132288362
original gDNA sequence snippet TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered gDNA sequence snippet TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
original cDNA sequence snippet TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered cDNA sequence snippet TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
wildtype AA sequence MSGAGVAAGT RPPSSPTPGS RRRRQRPSVG VQSLRPQSPQ LRQSDPQKRN LDLEKSLQFL
QQQHSEMLAK LHEEIEHLKR ENKDLHYKLI MNQTSQKKDG PSGNHLSRAS APLGARWVCI
NGVWVEPGGP SPARLKEGSS RTHRPGGKRG RLAGGSADTV RSPADSLSMS SFQSVKSISN
SGKARPQPGS FNKQDSKADV SQKADLEEEP LLHNSKLDKV PGVQGQARKE KAEASNAGAA
CMGNSQHQGR QMGAGAHPPM ILPLPLRKPT TLRQCEVLIR ELWNTNLLQT QELRHLKSLL
EGSQRPQAAP EEASFPRDQE ATHFPKVSTK SLSKKCLSPP VAERAILPAL KQTPKNNFAE
RQKRLQAMQK RRLHRSVL*
mutated AA sequence MSGAGVAAGT RPPSSPTPGS RRRRQRPSVG VQSLRPQSPQ LRQSDPQKRN LDLEKSLQFL
QQQHSEMLAK LHEEIEHLKR ENKDLHYKLI MNQTSQKKDG PSGNHLSRAS APLGARWVCI
NGVWVEPGGP SPARLKEGSS RTHRPGGKRG RLAGGSADTV RSPADSLSTS SFQSVKSISN
SGKARPQPGS FNKQDSKADV SQKADLEEEP LLHNSKLDKV PGVQGQARKE KAEASNAGAA
CMGNSQHQGR QMGAGAHPPM ILPLPLRKPT TLRQCEVLIR ELWNTNLLQT QELRHLKSLL
EGSQRPQAAP EEASFPRDQE ATHFPKVSTK SLSKKCLSPP VAERAILPAL KQTPKNNFAE
RQKRLQAMQK RRLHRSVL*
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: 0.999999999999996 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:132288362T>CN/A show variant in all transcripts   IGV
HGNC symbol CCDC74A
Ensembl transcript ID ENST00000467992
Genbank transcript ID N/A
UniProt peptide Q96LY2
alteration type single base exchange
alteration region CDS
DNA changes c.812T>C
cDNA.1126T>C
g.3115T>C
AA changes M271T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
271
frameshift no
known variant Reference ID: rs201632382
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC48171723122048
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.410.004
-0.5290.001
(flanking)-1.8630
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 increased3115wt: 0.2715 / mu: 0.2836 (marginal change - not scored)wt: TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
mu: TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
 ccat|GTCA
Donor increased3110wt: 0.58 / mu: 0.76wt: AGCCTCTCCATGTCA
mu: AGCCTCTCCACGTCA
 CCTC|tcca
Donor marginally increased3115wt: 0.9978 / mu: 0.9983 (marginal change - not scored)wt: CTCCATGTCAAGCTT
mu: CTCCACGTCAAGCTT
 CCAT|gtca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      271DTVRSPADSLSMSSFQSVKSISNS
mutated  not conserved    271DTVRSPADSLSTSSFQSVKSISN
Ptroglodytes  not conserved  ENSPTRG00000012471  169TVRSPADSLSTSSFQSVKSISN
Mmulatta  not conserved  ENSMMUG00000003066  266D-LRSPADSLSTSSFPSVKSISN
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000041617  106SISTWSLHSGKSASN
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000093026  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 993 / 993
position (AA) of stopcodon in wt / mu AA sequence 331 / 331
position of stopcodon in wt / mu cDNA 1307 / 1307
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 315 / 315
chromosome 2
strand 1
last intron/exon boundary 2414
theoretical NMD boundary in CDS 2049
length of CDS 993
coding sequence (CDS) position 812
cDNA position
(for ins/del: last normal base / first normal base)
1126
gDNA position
(for ins/del: last normal base / first normal base)
3115
chromosomal position
(for ins/del: last normal base / first normal base)
132288362
original gDNA sequence snippet TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered gDNA sequence snippet TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
original cDNA sequence snippet TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered cDNA sequence snippet TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
wildtype AA sequence MGRNPWDSPC PARSLPQIAA VARPRISSPM ALSPHMLGAQ GLWTHSIQGS LPAIWAATMG
TKGGSRVLFP CHLSKALPHP DSGPHPAQDP GLWSQAHFPL SLGLGLTSGG HLTGGWSQPG
NIAAGAVPRA LPSQGDMEKG VEGGPFPSRC GNSSELFWAK CGPSRQPQPC SAGDADRTRE
EAMLSLGTCC SMCPKPSCFP DGPSGNHLSR ASAPLGARWV CINGVWVEPG GPSPARLKEG
SSRTHRPGGK RGRLAGGSAD TVRSPADSLS MSSFQSVKSI SNSGKARPQP GSFNKQDSKA
DVSQKADLEE EPLLHNSKLD KVPGVQGQAR *
mutated AA sequence MGRNPWDSPC PARSLPQIAA VARPRISSPM ALSPHMLGAQ GLWTHSIQGS LPAIWAATMG
TKGGSRVLFP CHLSKALPHP DSGPHPAQDP GLWSQAHFPL SLGLGLTSGG HLTGGWSQPG
NIAAGAVPRA LPSQGDMEKG VEGGPFPSRC GNSSELFWAK CGPSRQPQPC SAGDADRTRE
EAMLSLGTCC SMCPKPSCFP DGPSGNHLSR ASAPLGARWV CINGVWVEPG GPSPARLKEG
SSRTHRPGGK RGRLAGGSAD TVRSPADSLS TSSFQSVKSI SNSGKARPQP GSFNKQDSKA
DVSQKADLEE EPLLHNSKLD KVPGVQGQAR *
speed 1.40 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: 0.999999999999996 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:132288362T>CN/A show variant in all transcripts   IGV
HGNC symbol CCDC74A
Ensembl transcript ID ENST00000409856
Genbank transcript ID NM_001258306
UniProt peptide Q96LY2
alteration type single base exchange
alteration region CDS
DNA changes c.308T>C
cDNA.399T>C
g.3115T>C
AA changes M103T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
103
frameshift no
known variant Reference ID: rs201632382
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC48171723122048
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.410.004
-0.5290.001
(flanking)-1.8630
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 increased3115wt: 0.2715 / mu: 0.2836 (marginal change - not scored)wt: TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
mu: TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
 ccat|GTCA
Donor increased3110wt: 0.58 / mu: 0.76wt: AGCCTCTCCATGTCA
mu: AGCCTCTCCACGTCA
 CCTC|tcca
Donor marginally increased3115wt: 0.9978 / mu: 0.9983 (marginal change - not scored)wt: CTCCATGTCAAGCTT
mu: CTCCACGTCAAGCTT
 CCAT|gtca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      103NQTSQKKDSLSMSSFQSVKSISNS
mutated  not conserved    103NQTSQKKDSLSTSSFQSVKSISN
Ptroglodytes  not conserved  ENSPTRG00000012471  132DTVRSPADSLSTSSFQSVKSISN
Mmulatta  not conserved  ENSMMUG00000003066  265DSLSTSSFPSVKSISN
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000041617  106NEKPQKKGSISTWSLHSGKSASN
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000093026  58EPPNSSRKG---SSCKI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 939 / 939
position (AA) of stopcodon in wt / mu AA sequence 313 / 313
position of stopcodon in wt / mu cDNA 1030 / 1030
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 92 / 92
chromosome 2
strand 1
last intron/exon boundary 901
theoretical NMD boundary in CDS 759
length of CDS 939
coding sequence (CDS) position 308
cDNA position
(for ins/del: last normal base / first normal base)
399
gDNA position
(for ins/del: last normal base / first normal base)
3115
chromosomal position
(for ins/del: last normal base / first normal base)
132288362
original gDNA sequence snippet TCCTGCAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered gDNA sequence snippet TCCTGCAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
original cDNA sequence snippet GAAGAAAGACAGCCTCTCCATGTCAAGCTTCCAGTCTGTCA
altered cDNA sequence snippet GAAGAAAGACAGCCTCTCCACGTCAAGCTTCCAGTCTGTCA
wildtype AA sequence MSGAGVAAGT RPPSSPTPGS RRRRQRPSVG VQSLRPQSPQ LRQSDPQKRN LDLEKSLQFL
QQQHSEMLAK LHEEIEHLKR ENKDLHYKLI MNQTSQKKDS LSMSSFQSVK SISNSGKARP
QPGSFNKQDS KADVSQKADL EEEPLLHNSK LDKVPGVQGQ ARKEKAEASN AGAACMGNSQ
HQGRQMGAGA HPPMILPLPL RKPTTLRQCE VLIRELWNTN LLQTQELRHL KSLLEGSQRP
QAAPEEASFP RDQEATHFPK VSTKSLSKKC LSPPVAERAI LPALKQTPKN NFAERQKRLQ
AMQKRRLHRS VL*
mutated AA sequence MSGAGVAAGT RPPSSPTPGS RRRRQRPSVG VQSLRPQSPQ LRQSDPQKRN LDLEKSLQFL
QQQHSEMLAK LHEEIEHLKR ENKDLHYKLI MNQTSQKKDS LSTSSFQSVK SISNSGKARP
QPGSFNKQDS KADVSQKADL EEEPLLHNSK LDKVPGVQGQ ARKEKAEASN AGAACMGNSQ
HQGRQMGAGA HPPMILPLPL RKPTTLRQCE VLIRELWNTN LLQTQELRHL KSLLEGSQRP
QAAPEEASFP RDQEATHFPK VSTKSLSKKC LSPPVAERAI LPALKQTPKN NFAERQKRLQ
AMQKRRLHRS VL*
speed 1.24 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

annotation problem

back to results table