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: ENST00000305202
Querying Taster for transcript #2: ENST00000565691
MT speed 3.06 s - this script 7.99259 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
NECAB2polymorphism_automatic5.39609468219737e-11simple_aaeaffectedT152Ssingle base exchangers2292324show file
NECAB2polymorphism_automatic5.39609468219737e-11simple_aaeaffectedT235Ssingle base exchangers2292324show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999946039 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:84028014C>GN/A show variant in all transcripts   IGV
HGNC symbol NECAB2
Ensembl transcript ID ENST00000565691
Genbank transcript ID N/A
UniProt peptide Q7Z6G3
alteration type single base exchange
alteration region CDS
DNA changes c.455C>G
cDNA.1177C>G
g.25778C>G
AA changes T152S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
152
frameshift no
known variant Reference ID: rs2292324
databasehomozygous (G/G)heterozygousallele carriers
1000G196730926
ExAC18131345915272
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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)0.3630.446
0.5570.36
(flanking)0.4150.261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased25788wt: 0.91 / mu: 0.82wt: CAAGGCAAGACCCTTCCATCTGGTGAGAGAAAGCGGGGGCC
mu: CAAGGCAAGAGCCTTCCATCTGGTGAGAGAAAGCGGGGGCC
 atct|GGTG
Donor gained257720.72mu: ACAAGGCAAGAGCCT AAGG|caag
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152NHKLMAMEQGKTLPSATEDAKEEG
mutated  all conserved    152NHKLMAMEQGKSLPSATEDAKEE
Ptroglodytes  all conserved  ENSPTRG00000008406  235NHKLMAMEQGKSLPSAT
Mmulatta  not conserved  ENSMMUG00000029071  170NHKLMAVEQGKGLPSAT
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000031837  238NHKLVAPEPMKSLPVAT
Ggallus  all conserved  ENSGALG00000003309  233PGRIVPRGHGKSSQSGA
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000056745  274NNRVSAKESMRNINTGA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
170201COILEDPotential.might get lost (downstream of altered splice site)
283384DOMAINABM.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 912 / 912
position (AA) of stopcodon in wt / mu AA sequence 304 / 304
position of stopcodon in wt / mu cDNA 1634 / 1634
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 723 / 723
chromosome 16
strand 1
last intron/exon boundary 1606
theoretical NMD boundary in CDS 833
length of CDS 912
coding sequence (CDS) position 455
cDNA position
(for ins/del: last normal base / first normal base)
1177
gDNA position
(for ins/del: last normal base / first normal base)
25778
chromosomal position
(for ins/del: last normal base / first normal base)
84028014
original gDNA sequence snippet GGCTATGGAACAAGGCAAGACCCTTCCATCTGGTGAGAGAA
altered gDNA sequence snippet GGCTATGGAACAAGGCAAGAGCCTTCCATCTGGTGAGAGAA
original cDNA sequence snippet GGCTATGGAACAAGGCAAGACCCTTCCATCTGCCACGGAGG
altered cDNA sequence snippet GGCTATGGAACAAGGCAAGAGCCTTCCATCTGCCACGGAGG
wildtype AA sequence MMMGSCPWRN SSSSLQMASL MRKNWRISFT RLTLTTPNYF VDHMGDYEDV LASLETLNHS
VLKAMGYTKK VYEGGSNVDQ FVTRFLLKET ANQIQSLLSS VESAVEAIEE QTSQLRQNHI
KPSHSAAQTW CGSPTPASAP NHKLMAMEQG KTLPSATEDA KEEGLEAQIS RLAELIGRLE
SKALWFDLQQ RLSDEDGTNM HLQLVRQEMA VCPEQLSEFL DSLRQYLRGT TGVRNCFHIT
AVRLSDGFTF VIYEFWETEE AWKRHLQSPL CKAFRHVKVD TLSQPEALSR ILVPAAWCTV
GRD*
mutated AA sequence MMMGSCPWRN SSSSLQMASL MRKNWRISFT RLTLTTPNYF VDHMGDYEDV LASLETLNHS
VLKAMGYTKK VYEGGSNVDQ FVTRFLLKET ANQIQSLLSS VESAVEAIEE QTSQLRQNHI
KPSHSAAQTW CGSPTPASAP NHKLMAMEQG KSLPSATEDA KEEGLEAQIS RLAELIGRLE
SKALWFDLQQ RLSDEDGTNM HLQLVRQEMA VCPEQLSEFL DSLRQYLRGT TGVRNCFHIT
AVRLSDGFTF VIYEFWETEE AWKRHLQSPL CKAFRHVKVD TLSQPEALSR ILVPAAWCTV
GRD*
speed 1.41 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: 0.999999999946039 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:84028014C>GN/A show variant in all transcripts   IGV
HGNC symbol NECAB2
Ensembl transcript ID ENST00000305202
Genbank transcript ID NM_019065
UniProt peptide Q7Z6G3
alteration type single base exchange
alteration region CDS
DNA changes c.704C>G
cDNA.721C>G
g.25778C>G
AA changes T235S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
235
frameshift no
known variant Reference ID: rs2292324
databasehomozygous (G/G)heterozygousallele carriers
1000G196730926
ExAC18131345915272
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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)0.3630.446
0.5570.36
(flanking)0.4150.261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased25788wt: 0.91 / mu: 0.82wt: CAAGGCAAGACCCTTCCATCTGGTGAGAGAAAGCGGGGGCC
mu: CAAGGCAAGAGCCTTCCATCTGGTGAGAGAAAGCGGGGGCC
 atct|GGTG
Donor gained257720.72mu: ACAAGGCAAGAGCCT AAGG|caag
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235NHKLMAMEQGKTLPSATEDAKEEG
mutated  all conserved    235NHKLMAMEQGKSLPSAT
Ptroglodytes  all conserved  ENSPTRG00000008406  235NHKLMAMEQGKSLPSAT
Mmulatta  not conserved  ENSMMUG00000029071  170NHKLMAVEQGKGLPSATEDAKE
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000031837  238NHKLVAPEPMKSLP
Ggallus  all conserved  ENSGALG00000003309  233PGRIVPRGHGKSSQSGA
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000056745  274NNRVSAKESMRNINTGAGAVEVRKE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
283384DOMAINABM.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1161 / 1161
position (AA) of stopcodon in wt / mu AA sequence 387 / 387
position of stopcodon in wt / mu cDNA 1178 / 1178
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 18 / 18
chromosome 16
strand 1
last intron/exon boundary 1150
theoretical NMD boundary in CDS 1082
length of CDS 1161
coding sequence (CDS) position 704
cDNA position
(for ins/del: last normal base / first normal base)
721
gDNA position
(for ins/del: last normal base / first normal base)
25778
chromosomal position
(for ins/del: last normal base / first normal base)
84028014
original gDNA sequence snippet GGCTATGGAACAAGGCAAGACCCTTCCATCTGGTGAGAGAA
altered gDNA sequence snippet GGCTATGGAACAAGGCAAGAGCCTTCCATCTGGTGAGAGAA
original cDNA sequence snippet GGCTATGGAACAAGGCAAGACCCTTCCATCTGCCACGGAGG
altered cDNA sequence snippet GGCTATGGAACAAGGCAAGAGCCTTCCATCTGCCACGGAGG
wildtype AA sequence MCERAARLCR AGAHRLLREP PQQGRALGGL LRWVGARMGE PRESLAPAAP ADPGPASPRG
GTAVILDIFR RADKNDDGKL SLEEFQLFFA DGVLNEKELE DLFHTIDSDN TNHVDTKELC
DYFVDHMGDY EDVLASLETL NHSVLKAMGY TKKVYEGGSN VDQFVTRFLL KETANQIQSL
LSSVESAVEA IEEQTSQLRQ NHIKPSHSAA QTWCGSPTPA SAPNHKLMAM EQGKTLPSAT
EDAKEEGLEA QISRLAELIG RLESKALWFD LQQRLSDEDG TNMHLQLVRQ EMAVCPEQLS
EFLDSLRQYL RGTTGVRNCF HITAVRLSDG FTFVIYEFWE TEEAWKRHLQ SPLCKAFRHV
KVDTLSQPEA LSRILVPAAW CTVGRD*
mutated AA sequence MCERAARLCR AGAHRLLREP PQQGRALGGL LRWVGARMGE PRESLAPAAP ADPGPASPRG
GTAVILDIFR RADKNDDGKL SLEEFQLFFA DGVLNEKELE DLFHTIDSDN TNHVDTKELC
DYFVDHMGDY EDVLASLETL NHSVLKAMGY TKKVYEGGSN VDQFVTRFLL KETANQIQSL
LSSVESAVEA IEEQTSQLRQ NHIKPSHSAA QTWCGSPTPA SAPNHKLMAM EQGKSLPSAT
EDAKEEGLEA QISRLAELIG RLESKALWFD LQQRLSDEDG TNMHLQLVRQ EMAVCPEQLS
EFLDSLRQYL RGTTGVRNCF HITAVRLSDG FTFVIYEFWE TEEAWKRHLQ SPLCKAFRHV
KVDTLSQPEA LSRILVPAAW CTVGRD*
speed 1.65 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