Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000302190
Querying Taster for transcript #2: ENST00000518385
Querying Taster for transcript #3: ENST00000522911
Querying Taster for transcript #4: ENST00000519914
Querying Taster for transcript #5: ENST00000545117
MT speed 7.1 s - this script 7.656956 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SDC2polymorphism_automatic0.773177376757459simple_aaeaffectedS35Tsingle base exchangers1042381show file
SDC2polymorphism_automatic0.976096565519388simple_aaeaffectedS71Tsingle base exchangers1042381show file
SDC2polymorphism_automatic0.976096565519388simple_aaeaffectedS71Tsingle base exchangers1042381show file
SDC2polymorphism_automatic0.988498394981143simple_aaeaffectedS42Tsingle base exchangers1042381show file
SDC2polymorphism_automatic0.988498394981143simple_aaeaffectedS42Tsingle base exchangers1042381show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.226822623242541 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000518385
Genbank transcript ID N/A
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.103T>A
cDNA.562T>A
g.109083T>A
AA changes S35T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
35
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC
 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      35DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    35DEDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71EDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71EDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFTSA
Mmusculus  all identical  ENSMUSG00000022261  71EDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70EEDEDSTVTTTSRIVPKLPTTSD
Trubripes  no alignment  ENSTRUG00000004101  n/a
Drerio  not conserved  ENSDARG00000002731  35SA-AKSPSTTDDLYLEEAGSGGYPEDDDDFSSGSGSG
Dmelanogaster  all conserved  FBgn0010415  218NSIATTPASTTTAAATQI--SSF
Celegans  no alignment  F57C7.3  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
4141CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5555CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5757CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 498 / 498
position (AA) of stopcodon in wt / mu AA sequence 166 / 166
position of stopcodon in wt / mu cDNA 957 / 957
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 460 / 460
chromosome 8
strand 1
last intron/exon boundary 794
theoretical NMD boundary in CDS 284
length of CDS 498
coding sequence (CDS) position 103
cDNA position
(for ins/del: last normal base / first normal base)
562
gDNA position
(for ins/del: last normal base / first normal base)
109083
chromosomal position
(for ins/del: last normal base / first normal base)
97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MRRAWILLTL GLVACVSAES VRADEDVESP ELTTSRPLPK ILLTSAAPKV ETTTLNIQNK
IPAQTKSPEE TDKEKVHLSD SERKMDPAEE DTNVYTEKHS DSLFKRTEVL AAVIAGGVIG
FLFAIFLILL LVYRMRKKDE GSYDLGERKP SSAAYQKAPT KEFYA*
mutated AA sequence MRRAWILLTL GLVACVSAES VRADEDVESP ELTTTRPLPK ILLTSAAPKV ETTTLNIQNK
IPAQTKSPEE TDKEKVHLSD SERKMDPAEE DTNVYTEKHS DSLFKRTEVL AAVIAGGVIG
FLFAIFLILL LVYRMRKKDE GSYDLGERKP SSAAYQKAPT KEFYA*
speed 1.52 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: 0.023903434480612 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000302190
Genbank transcript ID NM_002998
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.211T>A
cDNA.1132T>A
g.109083T>A
AA changes S71T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
71
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC
 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    71EDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71EDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71EDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFT
Mmusculus  all identical  ENSMUSG00000022261  71EDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70STVTTTSRIVPKLPTTSD
Trubripes  all identical  ENSTRUG00000004101  68GEEVVEEAVTISTVYIK------
Drerio  not conserved  ENSDARG00000002731  72GEVIEDPVTVNTLFFVPKAEPTQD
Dmelanogaster  no alignment  FBgn0010415  n/a
Celegans  not conserved  F57C7.3  100PPSSATTKSDKVTSPSHAVVTAK
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 606 / 606
position (AA) of stopcodon in wt / mu AA sequence 202 / 202
position of stopcodon in wt / mu cDNA 1527 / 1527
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 922 / 922
chromosome 8
strand 1
last intron/exon boundary 1364
theoretical NMD boundary in CDS 392
length of CDS 606
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)
1132
gDNA position
(for ins/del: last normal base / first normal base)
109083
chromosomal position
(for ins/del: last normal base / first normal base)
97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT SRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
mutated AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT TRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
speed 1.49 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: 0.023903434480612 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000545117
Genbank transcript ID N/A
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.211T>A
cDNA.630T>A
g.109083T>A
AA changes S71T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
71
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC
 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    71EDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71EDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71EDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFT
Mmusculus  all identical  ENSMUSG00000022261  71EDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70STVTTTSRIVPKLPTTSD
Trubripes  all identical  ENSTRUG00000004101  68GEEVVEEAVTISTVYIK------
Drerio  not conserved  ENSDARG00000002731  72GEVIEDPVTVNTLFFVPKAEPTQD
Dmelanogaster  no alignment  FBgn0010415  n/a
Celegans  not conserved  F57C7.3  100PPSSATTKSDKVTSPSHAVVTAK
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 606 / 606
position (AA) of stopcodon in wt / mu AA sequence 202 / 202
position of stopcodon in wt / mu cDNA 1025 / 1025
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 420 / 420
chromosome 8
strand 1
last intron/exon boundary 862
theoretical NMD boundary in CDS 392
length of CDS 606
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)
630
gDNA position
(for ins/del: last normal base / first normal base)
109083
chromosomal position
(for ins/del: last normal base / first normal base)
97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT SRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
mutated AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT TRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
speed 1.27 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: 0.011501605018857 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000522911
Genbank transcript ID N/A
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.124T>A
cDNA.187T>A
g.109083T>A
AA changes S42T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
42
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC
 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    42DEDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71DEDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71DEDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFTSA
Mmusculus  all identical  ENSMUSG00000022261  71DEDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70EEDEDSTVTTTSRIVPKLPTTSD
Trubripes  all identical  ENSTRUG00000004101  68GEEVVEEAVTISTVYIK------
Drerio  not conserved  ENSDARG00000002731  71GEVIEDPVTVNTLFFVPKAEPTQD
Dmelanogaster  not conserved  FBgn0010415  209DIGGHSTGINSIATTPASTTTAA
Celegans  not conserved  F57C7.3  100PPSSATTKSDKVTSPSHAVVTAK
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
4141CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5555CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5757CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 519 / 519
position (AA) of stopcodon in wt / mu AA sequence 173 / 173
position of stopcodon in wt / mu cDNA 582 / 582
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 64 / 64
chromosome 8
strand 1
last intron/exon boundary 419
theoretical NMD boundary in CDS 305
length of CDS 519
coding sequence (CDS) position 124
cDNA position
(for ins/del: last normal base / first normal base)
187
gDNA position
(for ins/del: last normal base / first normal base)
109083
chromosomal position
(for ins/del: last normal base / first normal base)
97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TSRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*
mutated AA sequence MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TTRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*
speed 1.28 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: 0.011501605018857 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000519914
Genbank transcript ID N/A
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.124T>A
cDNA.371T>A
g.109083T>A
AA changes S42T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
42
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC
 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    42DEDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71DEDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71DEDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFTSA
Mmusculus  all identical  ENSMUSG00000022261  71DEDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70EEDEDSTVTTTSRIVPKLPTTSD
Trubripes  all identical  ENSTRUG00000004101  68GEEVVEEAVTISTVYIK------
Drerio  not conserved  ENSDARG00000002731  71GEVIEDPVTVNTLFFVPKAEPTQD
Dmelanogaster  not conserved  FBgn0010415  209DIGGHSTGINSIATTPASTTTAA
Celegans  not conserved  F57C7.3  100PPSSATTKSDKVTSPSHAVVTAK
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
4141CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5555CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
5757CARBOHYDO-linked (Xyl...) (heparan sulfate) (Potential).might get lost (downstream of altered splice site)
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 519 / 519
position (AA) of stopcodon in wt / mu AA sequence 173 / 173
position of stopcodon in wt / mu cDNA 766 / 766
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 248 / 248
chromosome 8
strand 1
last intron/exon boundary 603
theoretical NMD boundary in CDS 305
length of CDS 519
coding sequence (CDS) position 124
cDNA position
(for ins/del: last normal base / first normal base)
371
gDNA position
(for ins/del: last normal base / first normal base)
109083
chromosomal position
(for ins/del: last normal base / first normal base)
97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TSRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*
mutated AA sequence MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TTRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*
speed 1.54 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