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 9 transcript(s)...
Querying Taster for transcript #1: ENST00000324631
Querying Taster for transcript #2: ENST00000352115
Querying Taster for transcript #3: ENST00000377328
Querying Taster for transcript #4: ENST00000282343
Querying Taster for transcript #5: ENST00000377331
Querying Taster for transcript #6: ENST00000396576
Querying Taster for transcript #7: ENST00000377319
Querying Taster for transcript #8: ENST00000377329
Querying Taster for transcript #9: ENST00000377315
MT speed 0 s - this script 7.509297 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CACNB2disease_causing_automatic0.797258979944361simple_aaeaffected0S285Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S535Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S511Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S483Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S507Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S480Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S442Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S481Lsingle base exchangers121917812show file
CACNB2disease_causing_automatic0.99088918119389simple_aaeaffected0S487Lsingle base exchangers121917812show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.797258979944361 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000377328
Genbank transcript ID N/A
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.854C>T
cDNA.854C>T
g.398669C>T
AA changes S285L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 285
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      285PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    285PVKKSQHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  not conserved  ENSMUSG00000057914  531PVKKSQHRSSS-ATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  488PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  488STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  499EEEEEEDDDEENTDQRHDNRDQQNHHKNQHSSSTRTERHH
Dmelanogaster  not conserved  FBgn0259822  537----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
364364CONFLICTL -> V (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
406406CONFLICTR -> T (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1233 / 1233
position (AA) of stopcodon in wt / mu AA sequence 411 / 411
position of stopcodon in wt / mu cDNA 1233 / 1233
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 1 / 1
chromosome 10
strand 1
last intron/exon boundary 739
theoretical NMD boundary in CDS 688
length of CDS 1233
coding sequence (CDS) position 854
cDNA position
(for ins/del: last normal base / first normal base)		 854
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEVLQRLIKS RGKSQAKHLN VQMVAADKLA
QCPPELFDVI LDENQLEDAC EHLADYLEAY WKATHPPSSS LPNPLLSRTL ATSSLPLSPT
LASNSQGSQG DQRTDRSAPI RSASQAEEEP SVEPVKKSQH RSSSSAPHHN HRSGTSRGLS
RQETFDSETQ ESRDSAYVEP KEDYSHDHVD HYASHRDHNH RDETHGSSDH RHRESRHRSR
DVDREQDHNE CNKQRSRHKS KDRYCEKDGE VISKKRNEAG EWNRDVYIRQ *
mutated AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEVLQRLIKS RGKSQAKHLN VQMVAADKLA
QCPPELFDVI LDENQLEDAC EHLADYLEAY WKATHPPSSS LPNPLLSRTL ATSSLPLSPT
LASNSQGSQG DQRTDRSAPI RSASQAEEEP SVEPVKKSQH RSSSLAPHHN HRSGTSRGLS
RQETFDSETQ ESRDSAYVEP KEDYSHDHVD HYASHRDHNH RDETHGSSDH RHRESRHRSR
DVDREQDHNE CNKQRSRHKS KDRYCEKDGE VISKKRNEAG EWNRDVYIRQ *
speed 0.84 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000324631
Genbank transcript ID NM_201596
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1604C>T
cDNA.1664C>T
g.398669C>T
AA changes S535L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 535
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      535PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    535PVKKSQHRSSSLAPHHN
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHN
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHN
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQ
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  511ENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  539----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1983 / 1983
position (AA) of stopcodon in wt / mu AA sequence 661 / 661
position of stopcodon in wt / mu cDNA 2043 / 2043
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 61 / 61
chromosome 10
strand 1
last intron/exon boundary 1549
theoretical NMD boundary in CDS 1438
length of CDS 1983
coding sequence (CDS) position 1604
cDNA position
(for ins/del: last normal base / first normal base)		 1664
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEKFNNDWWI GRLVKEGCEI GFIPSPVKLE
NMRLQHEQRA KQGKFYSSKS GGNSSSSLGD IVPSSRKSTP PSSAIDIDAT GLDAEENDIP
ANHRSPKPSA NSVTSPHSKE KRMPFFKKTE HTPPYDVVPS MRPVVLVGPS LKGYEVTDMM
QKALFDFLKH RFEGRISITR VTADISLAKR SVLNNPSKHA IIERSNTRSS LAEVQSEIER
IFELARTLQL VVLDADTINH PAQLSKTSLA PIIVYVKISS PKVLQRLIKS RGKSQAKHLN
VQMVAADKLA QCPPELFDVI LDENQLEDAC EHLADYLEAY WKATHPPSSS LPNPLLSRTL
ATSSLPLSPT LASNSQGSQG DQRTDRSAPI RSASQAEEEP SVEPVKKSQH RSSSSAPHHN
HRSGTSRGLS RQETFDSETQ ESRDSAYVEP KEDYSHDHVD HYASHRDHNH RDETHGSSDH
RHRESRHRSR DVDREQDHNE CNKQRSRHKS KDRYCEKDGE VISKKRNEAG EWNRDVYIRQ
*
mutated AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEKFNNDWWI GRLVKEGCEI GFIPSPVKLE
NMRLQHEQRA KQGKFYSSKS GGNSSSSLGD IVPSSRKSTP PSSAIDIDAT GLDAEENDIP
ANHRSPKPSA NSVTSPHSKE KRMPFFKKTE HTPPYDVVPS MRPVVLVGPS LKGYEVTDMM
QKALFDFLKH RFEGRISITR VTADISLAKR SVLNNPSKHA IIERSNTRSS LAEVQSEIER
IFELARTLQL VVLDADTINH PAQLSKTSLA PIIVYVKISS PKVLQRLIKS RGKSQAKHLN
VQMVAADKLA QCPPELFDVI LDENQLEDAC EHLADYLEAY WKATHPPSSS LPNPLLSRTL
ATSSLPLSPT LASNSQGSQG DQRTDRSAPI RSASQAEEEP SVEPVKKSQH RSSSLAPHHN
HRSGTSRGLS RQETFDSETQ ESRDSAYVEP KEDYSHDHVD HYASHRDHNH RDETHGSSDH
RHRESRHRSR DVDREQDHNE CNKQRSRHKS KDRYCEKDGE VISKKRNEAG EWNRDVYIRQ
*
speed 0.88 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000352115
Genbank transcript ID NM_201597
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1532C>T
cDNA.1532C>T
g.398669C>T
AA changes S511L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 511
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      511PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    511PVKKSQHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHN
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHN
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQ
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  509DEENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  531------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1911 / 1911
position (AA) of stopcodon in wt / mu AA sequence 637 / 637
position of stopcodon in wt / mu cDNA 1911 / 1911
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 1 / 1
chromosome 10
strand 1
last intron/exon boundary 1417
theoretical NMD boundary in CDS 1366
length of CDS 1911
coding sequence (CDS) position 1532
cDNA position
(for ins/del: last normal base / first normal base)		 1532
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEKFNNDWWI GRLVKEGCEI GFIPSPVKLE
NMRLQHEQRA KQGKFYSSKS GGNSSSSLGD IVPSSRKSTP PSSGAKSADE QDQWKTAGLF
WRFTTEHTPP YDVVPSMRPV VLVGPSLKGY EVTDMMQKAL FDFLKHRFEG RISITRVTAD
ISLAKRSVLN NPSKHAIIER SNTRSSLAEV QSEIERIFEL ARTLQLVVLD ADTINHPAQL
SKTSLAPIIV YVKISSPKVL QRLIKSRGKS QAKHLNVQMV AADKLAQCPP ELFDVILDEN
QLEDACEHLA DYLEAYWKAT HPPSSSLPNP LLSRTLATSS LPLSPTLASN SQGSQGDQRT
DRSAPIRSAS QAEEEPSVEP VKKSQHRSSS SAPHHNHRSG TSRGLSRQET FDSETQESRD
SAYVEPKEDY SHDHVDHYAS HRDHNHRDET HGSSDHRHRE SRHRSRDVDR EQDHNECNKQ
RSRHKSKDRY CEKDGEVISK KRNEAGEWNR DVYIRQ*
mutated AA sequence MVQRDMSKSP PTAAAAVAQE IQMELLENVA PAGALGAAAQ SYGKGARRKN RFKGSDGSTS
SDTTSNSFVR QGSADSYTSR PSDSDVSLEE DREAVRREAE RQAQAQLEKA KTKPVAFAVR
TNVSYSAAHE DDVPVPGMAI SFEAKDFLHV KEKFNNDWWI GRLVKEGCEI GFIPSPVKLE
NMRLQHEQRA KQGKFYSSKS GGNSSSSLGD IVPSSRKSTP PSSGAKSADE QDQWKTAGLF
WRFTTEHTPP YDVVPSMRPV VLVGPSLKGY EVTDMMQKAL FDFLKHRFEG RISITRVTAD
ISLAKRSVLN NPSKHAIIER SNTRSSLAEV QSEIERIFEL ARTLQLVVLD ADTINHPAQL
SKTSLAPIIV YVKISSPKVL QRLIKSRGKS QAKHLNVQMV AADKLAQCPP ELFDVILDEN
QLEDACEHLA DYLEAYWKAT HPPSSSLPNP LLSRTLATSS LPLSPTLASN SQGSQGDQRT
DRSAPIRSAS QAEEEPSVEP VKKSQHRSSS LAPHHNHRSG TSRGLSRQET FDSETQESRD
SAYVEPKEDY SHDHVDHYAS HRDHNHRDET HGSSDHRHRE SRHRSRDVDR EQDHNECNKQ
RSRHKSKDRY CEKDGEVISK KRNEAGEWNR DVYIRQ*
speed 1.10 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000377331
Genbank transcript ID NM_201572
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1448C>T
cDNA.1448C>T
g.398669C>T
AA changes S483L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 483
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      483PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    483SSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  531PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  509DEENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  546---------------
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  509ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1827 / 1827
position (AA) of stopcodon in wt / mu AA sequence 609 / 609
position of stopcodon in wt / mu cDNA 1827 / 1827
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 1 / 1
chromosome 10
strand 1
last intron/exon boundary 1333
theoretical NMD boundary in CDS 1282
length of CDS 1827
coding sequence (CDS) position 1448
cDNA position
(for ins/del: last normal base / first normal base)		 1448
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MNQGSGLDLL KISYGKGARR KNRFKGSDGS TSSDTTSNSF VRQGSADSYT SRPSDSDVSL
EEDREAVRRE AERQAQAQLE KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL
HVKEKFNNDW WIGRLVKEGC EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL
GDIVPSSRKS TPPSSGAKSA DEQDQWKTAG LFWRFTTEHT PPYDVVPSMR PVVLVGPSLK
GYEVTDMMQK ALFDFLKHRF EGRISITRVT ADISLAKRSV LNNPSKHAII ERSNTRSSLA
EVQSEIERIF ELARTLQLVV LDADTINHPA QLSKTSLAPI IVYVKISSPK VLQRLIKSRG
KSQAKHLNVQ MVAADKLAQC PPELFDVILD ENQLEDACEH LADYLEAYWK ATHPPSSSLP
NPLLSRTLAT SSLPLSPTLA SNSQGSQGDQ RTDRSAPIRS ASQAEEEPSV EPVKKSQHRS
SSSAPHHNHR SGTSRGLSRQ ETFDSETQES RDSAYVEPKE DYSHDHVDHY ASHRDHNHRD
ETHGSSDHRH RESRHRSRDV DREQDHNECN KQRSRHKSKD RYCEKDGEVI SKKRNEAGEW
NRDVYIRQ*
mutated AA sequence MNQGSGLDLL KISYGKGARR KNRFKGSDGS TSSDTTSNSF VRQGSADSYT SRPSDSDVSL
EEDREAVRRE AERQAQAQLE KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL
HVKEKFNNDW WIGRLVKEGC EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL
GDIVPSSRKS TPPSSGAKSA DEQDQWKTAG LFWRFTTEHT PPYDVVPSMR PVVLVGPSLK
GYEVTDMMQK ALFDFLKHRF EGRISITRVT ADISLAKRSV LNNPSKHAII ERSNTRSSLA
EVQSEIERIF ELARTLQLVV LDADTINHPA QLSKTSLAPI IVYVKISSPK VLQRLIKSRG
KSQAKHLNVQ MVAADKLAQC PPELFDVILD ENQLEDACEH LADYLEAYWK ATHPPSSSLP
NPLLSRTLAT SSLPLSPTLA SNSQGSQGDQ RTDRSAPIRS ASQAEEEPSV EPVKKSQHRS
SSLAPHHNHR SGTSRGLSRQ ETFDSETQES RDSAYVEPKE DYSHDHVDHY ASHRDHNHRD
ETHGSSDHRH RESRHRSRDV DREQDHNECN KQRSRHKSKD RYCEKDGEVI SKKRNEAGEW
NRDVYIRQ*
speed 0.83 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000282343
Genbank transcript ID NM_201571
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1520C>T
cDNA.1742C>T
g.398669C>T
AA changes S507L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 507
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      507PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    507PVKKSQHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  531PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  511ENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  538----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  509ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1899 / 1899
position (AA) of stopcodon in wt / mu AA sequence 633 / 633
position of stopcodon in wt / mu cDNA 2121 / 2121
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 223 / 223
chromosome 10
strand 1
last intron/exon boundary 1627
theoretical NMD boundary in CDS 1354
length of CDS 1899
coding sequence (CDS) position 1520
cDNA position
(for ins/del: last normal base / first normal base)		 1742
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MNQGSGLDLL KISYGKGARR KNRFKGSDGS TSSDTTSNSF VRQGSADSYT SRPSDSDVSL
EEDREAVRRE AERQAQAQLE KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL
HVKEKFNNDW WIGRLVKEGC EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL
GDIVPSSRKS TPPSSAIDID ATGLDAEEND IPANHRSPKP SANSVTSPHS KEKRMPFFKK
TEHTPPYDVV PSMRPVVLVG PSLKGYEVTD MMQKALFDFL KHRFEGRISI TRVTADISLA
KRSVLNNPSK HAIIERSNTR SSLAEVQSEI ERIFELARTL QLVVLDADTI NHPAQLSKTS
LAPIIVYVKI SSPKVLQRLI KSRGKSQAKH LNVQMVAADK LAQCPPELFD VILDENQLED
ACEHLADYLE AYWKATHPPS SSLPNPLLSR TLATSSLPLS PTLASNSQGS QGDQRTDRSA
PIRSASQAEE EPSVEPVKKS QHRSSSSAPH HNHRSGTSRG LSRQETFDSE TQESRDSAYV
EPKEDYSHDH VDHYASHRDH NHRDETHGSS DHRHRESRHR SRDVDREQDH NECNKQRSRH
KSKDRYCEKD GEVISKKRNE AGEWNRDVYI RQ*
mutated AA sequence MNQGSGLDLL KISYGKGARR KNRFKGSDGS TSSDTTSNSF VRQGSADSYT SRPSDSDVSL
EEDREAVRRE AERQAQAQLE KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL
HVKEKFNNDW WIGRLVKEGC EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL
GDIVPSSRKS TPPSSAIDID ATGLDAEEND IPANHRSPKP SANSVTSPHS KEKRMPFFKK
TEHTPPYDVV PSMRPVVLVG PSLKGYEVTD MMQKALFDFL KHRFEGRISI TRVTADISLA
KRSVLNNPSK HAIIERSNTR SSLAEVQSEI ERIFELARTL QLVVLDADTI NHPAQLSKTS
LAPIIVYVKI SSPKVLQRLI KSRGKSQAKH LNVQMVAADK LAQCPPELFD VILDENQLED
ACEHLADYLE AYWKATHPPS SSLPNPLLSR TLATSSLPLS PTLASNSQGS QGDQRTDRSA
PIRSASQAEE EPSVEPVKKS QHRSSSLAPH HNHRSGTSRG LSRQETFDSE TQESRDSAYV
EPKEDYSHDH VDHYASHRDH NHRDETHGSS DHRHRESRHR SRDVDREQDH NECNKQRSRH
KSKDRYCEKD GEVISKKRNE AGEWNRDVYI RQ*
speed 1.15 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000396576
Genbank transcript ID NM_000724
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1439C>T
cDNA.1940C>T
g.398669C>T
AA changes S480L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 480
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      480PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    480PVKKSQHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  511ENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  539----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1818 / 1818
position (AA) of stopcodon in wt / mu AA sequence 606 / 606
position of stopcodon in wt / mu cDNA 2319 / 2319
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 502 / 502
chromosome 10
strand 1
last intron/exon boundary 1825
theoretical NMD boundary in CDS 1273
length of CDS 1818
coding sequence (CDS) position 1439
cDNA position
(for ins/del: last normal base / first normal base)		 1940
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MQCCGLVHRR RVRVSYGSAD SYTSRPSDSD VSLEEDREAV RREAERQAQA QLEKAKTKPV
AFAVRTNVSY SAAHEDDVPV PGMAISFEAK DFLHVKEKFN NDWWIGRLVK EGCEIGFIPS
PVKLENMRLQ HEQRAKQGKF YSSKSGGNSS SSLGDIVPSS RKSTPPSSAI DIDATGLDAE
ENDIPANHRS PKPSANSVTS PHSKEKRMPF FKKTEHTPPY DVVPSMRPVV LVGPSLKGYE
VTDMMQKALF DFLKHRFEGR ISITRVTADI SLAKRSVLNN PSKHAIIERS NTRSSLAEVQ
SEIERIFELA RTLQLVVLDA DTINHPAQLS KTSLAPIIVY VKISSPKVLQ RLIKSRGKSQ
AKHLNVQMVA ADKLAQCPPE LFDVILDENQ LEDACEHLAD YLEAYWKATH PPSSSLPNPL
LSRTLATSSL PLSPTLASNS QGSQGDQRTD RSAPIRSASQ AEEEPSVEPV KKSQHRSSSS
APHHNHRSGT SRGLSRQETF DSETQESRDS AYVEPKEDYS HDHVDHYASH RDHNHRDETH
GSSDHRHRES RHRSRDVDRE QDHNECNKQR SRHKSKDRYC EKDGEVISKK RNEAGEWNRD
VYIRQ*
mutated AA sequence MQCCGLVHRR RVRVSYGSAD SYTSRPSDSD VSLEEDREAV RREAERQAQA QLEKAKTKPV
AFAVRTNVSY SAAHEDDVPV PGMAISFEAK DFLHVKEKFN NDWWIGRLVK EGCEIGFIPS
PVKLENMRLQ HEQRAKQGKF YSSKSGGNSS SSLGDIVPSS RKSTPPSSAI DIDATGLDAE
ENDIPANHRS PKPSANSVTS PHSKEKRMPF FKKTEHTPPY DVVPSMRPVV LVGPSLKGYE
VTDMMQKALF DFLKHRFEGR ISITRVTADI SLAKRSVLNN PSKHAIIERS NTRSSLAEVQ
SEIERIFELA RTLQLVVLDA DTINHPAQLS KTSLAPIIVY VKISSPKVLQ RLIKSRGKSQ
AKHLNVQMVA ADKLAQCPPE LFDVILDENQ LEDACEHLAD YLEAYWKATH PPSSSLPNPL
LSRTLATSSL PLSPTLASNS QGSQGDQRTD RSAPIRSASQ AEEEPSVEPV KKSQHRSSSL
APHHNHRSGT SRGLSRQETF DSETQESRDS AYVEPKEDYS HDHVDHYASH RDHNHRDETH
GSSDHRHRES RHRSRDVDRE QDHNECNKQR SRHKSKDRYC EKDGEVISKK RNEAGEWNRD
VYIRQ*
speed 1.14 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000377319
Genbank transcript ID N/A
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1325C>T
cDNA.1334C>T
g.398669C>T
AA changes S442L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 442
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      442PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    442PVKKSQHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  511ENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  539----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1704 / 1704
position (AA) of stopcodon in wt / mu AA sequence 568 / 568
position of stopcodon in wt / mu cDNA 1713 / 1713
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 10 / 10
chromosome 10
strand 1
last intron/exon boundary 1219
theoretical NMD boundary in CDS 1159
length of CDS 1704
coding sequence (CDS) position 1325
cDNA position
(for ins/del: last normal base / first normal base)		 1334
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MQCCGLVHRR RVRVSYGSAD SYTSRPSDSD VSLEEDREAV RREAERQAQA QLEKAKTKPV
AFAVRTNVSY SAAHEDDVPV PGMAISFEAK DFLHVKEKFN NDWWIGRLVK EGCEIGFIPS
PVKLENMRLQ HEQRAKQGKF YSSKSGGNSS SSLGDIVPSS RKSTPPSSAK QKQKSTEHTP
PYDVVPSMRP VVLVGPSLKG YEVTDMMQKA LFDFLKHRFE GRISITRVTA DISLAKRSVL
NNPSKHAIIE RSNTRSSLAE VQSEIERIFE LARTLQLVVL DADTINHPAQ LSKTSLAPII
VYVKISSPKV LQRLIKSRGK SQAKHLNVQM VAADKLAQCP PELFDVILDE NQLEDACEHL
ADYLEAYWKA THPPSSSLPN PLLSRTLATS SLPLSPTLAS NSQGSQGDQR TDRSAPIRSA
SQAEEEPSVE PVKKSQHRSS SSAPHHNHRS GTSRGLSRQE TFDSETQESR DSAYVEPKED
YSHDHVDHYA SHRDHNHRDE THGSSDHRHR ESRHRSRDVD REQDHNECNK QRSRHKSKDR
YCEKDGEVIS KKRNEAGEWN RDVYIRQ*
mutated AA sequence MQCCGLVHRR RVRVSYGSAD SYTSRPSDSD VSLEEDREAV RREAERQAQA QLEKAKTKPV
AFAVRTNVSY SAAHEDDVPV PGMAISFEAK DFLHVKEKFN NDWWIGRLVK EGCEIGFIPS
PVKLENMRLQ HEQRAKQGKF YSSKSGGNSS SSLGDIVPSS RKSTPPSSAK QKQKSTEHTP
PYDVVPSMRP VVLVGPSLKG YEVTDMMQKA LFDFLKHRFE GRISITRVTA DISLAKRSVL
NNPSKHAIIE RSNTRSSLAE VQSEIERIFE LARTLQLVVL DADTINHPAQ LSKTSLAPII
VYVKISSPKV LQRLIKSRGK SQAKHLNVQM VAADKLAQCP PELFDVILDE NQLEDACEHL
ADYLEAYWKA THPPSSSLPN PLLSRTLATS SLPLSPTLAS NSQGSQGDQR TDRSAPIRSA
SQAEEEPSVE PVKKSQHRSS SLAPHHNHRS GTSRGLSRQE TFDSETQESR DSAYVEPKED
YSHDHVDHYA SHRDHNHRDE THGSSDHRHR ESRHRSRDVD REQDHNECNK QRSRHKSKDR
YCEKDGEVIS KKRNEAGEWN RDVYIRQ*
speed 1.08 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000377329
Genbank transcript ID NM_201590
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1442C>T
cDNA.1632C>T
g.398669C>T
AA changes S481L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 481
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      481PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    481LAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  487PIKKSHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  486STRTDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  510EENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHHHHHHRHHHSRTA
Dmelanogaster  not conserved  FBgn0259822  539----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  508ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1821 / 1821
position (AA) of stopcodon in wt / mu AA sequence 607 / 607
position of stopcodon in wt / mu cDNA 2011 / 2011
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 191 / 191
chromosome 10
strand 1
last intron/exon boundary 1517
theoretical NMD boundary in CDS 1276
length of CDS 1821
coding sequence (CDS) position 1442
cDNA position
(for ins/del: last normal base / first normal base)		 1632
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MLDRRLIAPQ TKYIIPGGSA DSYTSRPSDS DVSLEEDREA VRREAERQAQ AQLEKAKTKP
VAFAVRTNVS YSAAHEDDVP VPGMAISFEA KDFLHVKEKF NNDWWIGRLV KEGCEIGFIP
SPVKLENMRL QHEQRAKQGK FYSSKSGGNS SSSLGDIVPS SRKSTPPSSA IDIDATGLDA
EENDIPANHR SPKPSANSVT SPHSKEKRMP FFKKTEHTPP YDVVPSMRPV VLVGPSLKGY
EVTDMMQKAL FDFLKHRFEG RISITRVTAD ISLAKRSVLN NPSKHAIIER SNTRSSLAEV
QSEIERIFEL ARTLQLVVLD ADTINHPAQL SKTSLAPIIV YVKISSPKVL QRLIKSRGKS
QAKHLNVQMV AADKLAQCPP ELFDVILDEN QLEDACEHLA DYLEAYWKAT HPPSSSLPNP
LLSRTLATSS LPLSPTLASN SQGSQGDQRT DRSAPIRSAS QAEEEPSVEP VKKSQHRSSS
SAPHHNHRSG TSRGLSRQET FDSETQESRD SAYVEPKEDY SHDHVDHYAS HRDHNHRDET
HGSSDHRHRE SRHRSRDVDR EQDHNECNKQ RSRHKSKDRY CEKDGEVISK KRNEAGEWNR
DVYIRQ*
mutated AA sequence MLDRRLIAPQ TKYIIPGGSA DSYTSRPSDS DVSLEEDREA VRREAERQAQ AQLEKAKTKP
VAFAVRTNVS YSAAHEDDVP VPGMAISFEA KDFLHVKEKF NNDWWIGRLV KEGCEIGFIP
SPVKLENMRL QHEQRAKQGK FYSSKSGGNS SSSLGDIVPS SRKSTPPSSA IDIDATGLDA
EENDIPANHR SPKPSANSVT SPHSKEKRMP FFKKTEHTPP YDVVPSMRPV VLVGPSLKGY
EVTDMMQKAL FDFLKHRFEG RISITRVTAD ISLAKRSVLN NPSKHAIIER SNTRSSLAEV
QSEIERIFEL ARTLQLVVLD ADTINHPAQL SKTSLAPIIV YVKISSPKVL QRLIKSRGKS
QAKHLNVQMV AADKLAQCPP ELFDVILDEN QLEDACEHLA DYLEAYWKAT HPPSSSLPNP
LLSRTLATSS LPLSPTLASN SQGSQGDQRT DRSAPIRSAS QAEEEPSVEP VKKSQHRSSS
LAPHHNHRSG TSRGLSRQET FDSETQESRD SAYVEPKEDY SHDHVDHYAS HRDHNHRDET
HGSSDHRHRE SRHRSRDVDR EQDHNECNKQ RSRHKSKDRY CEKDGEVISK KRNEAGEWNR
DVYIRQ*
speed 1.11 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99088918119389 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070049)
  • known disease mutation: rs9547 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:18828274C>TN/A show variant in all transcripts   IGV
HGNC symbol CACNB2
Ensembl transcript ID ENST00000377315
Genbank transcript ID NM_201570
UniProt peptide Q08289
alteration type single base exchange
alteration region CDS
DNA changes c.1460C>T
cDNA.1679C>T
g.398669C>T
AA changes S487L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 487
frameshift no
known variant Reference ID: rs121917812
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9547 (pathogenic for Brugada syndrome 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070049)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8630.998
3.7331
(flanking)-1.8660.058
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 increased398669wt: 0.7660 / mu: 0.7730 (marginal change - not scored)wt: CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
mu: CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC		 cctc|AGCC
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      487PVKKSQHRSSSSAPHHNHRSGTSR
mutated  not conserved    487QHRSSSLAPHHNHRSGTS
Ptroglodytes  all identical  ENSPTRG00000002339  535PVKKSQHRSSSSAPHHNHRSGTS
Mmulatta  all identical  ENSMMUG00000007445  535PVKKSQHRSSSSAPHHNHRGGTS
Fcatus  all identical  ENSFCAG00000015492  495PVKKPHHRSSSSAQHHSHRGGTS
Mmusculus  all identical  ENSMUSG00000057914  532PVKKSQHR-SSSATHQNHRSGTG
Ggallus  not conserved  ENSGALG00000008591  488SHHRSSTQ--HHNHRSGV-
Trubripes  not conserved  ENSTRUG00000007932  488TDHHNHHHHHHHHHHHSGRA
Drerio  all conserved  ENSDARG00000079906  504EEEEEEDDDEENTDQRHDNRDQQNHHKNQHSSSTRTERHHHHRHHHH
Dmelanogaster  not conserved  FBgn0259822  539----------------DPRMGMS
Celegans  no alignment  T28F2.5  n/a
Xtropicalis  all identical  ENSXETG00000022755  509ATKKSHHRSSSSAQHHNHRSGGS
protein features
start (aa)end (aa)featuredetails 
501501CONFLICTD -> H (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
524524CONFLICTP -> G (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
549549SITERequired for CaMK2D-binding (By similarity).might get lost (downstream of altered splice site)
554554MOD_RESPhosphothreonine; by CaMK2D (By similarity).might get lost (downstream of altered splice site)
624624CONFLICTQ -> QQ (in Ref. 3; AAD33729/AAD33730).might get lost (downstream of altered splice site)
659659CONFLICTR -> P (in Ref. 2; AAB53332, 5; AAG01473/ AAL16948/AAL16951/AAL16950 and 6; AAL73495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1839 / 1839
position (AA) of stopcodon in wt / mu AA sequence 613 / 613
position of stopcodon in wt / mu cDNA 2058 / 2058
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 220 / 220
chromosome 10
strand 1
last intron/exon boundary 1564
theoretical NMD boundary in CDS 1294
length of CDS 1839
coding sequence (CDS) position 1460
cDNA position
(for ins/del: last normal base / first normal base)		 1679
gDNA position
(for ins/del: last normal base / first normal base)		 398669
chromosomal position
(for ins/del: last normal base / first normal base)		 18828274
original gDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered gDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
original cDNA sequence snippet CCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATC
altered cDNA sequence snippet CCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATC
wildtype AA sequence MKATWIRLLK RAKGGRLKNS DICGSADSYT SRPSDSDVSL EEDREAVRRE AERQAQAQLE
KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL HVKEKFNNDW WIGRLVKEGC
EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL GDIVPSSRKS TPPSSAIDID
ATGLDAEEND IPANHRSPKP SANSVTSPHS KEKRMPFFKK TEHTPPYDVV PSMRPVVLVG
PSLKGYEVTD MMQKALFDFL KHRFEGRISI TRVTADISLA KRSVLNNPSK HAIIERSNTR
SSLAEVQSEI ERIFELARTL QLVVLDADTI NHPAQLSKTS LAPIIVYVKI SSPKVLQRLI
KSRGKSQAKH LNVQMVAADK LAQCPPELFD VILDENQLED ACEHLADYLE AYWKATHPPS
SSLPNPLLSR TLATSSLPLS PTLASNSQGS QGDQRTDRSA PIRSASQAEE EPSVEPVKKS
QHRSSSSAPH HNHRSGTSRG LSRQETFDSE TQESRDSAYV EPKEDYSHDH VDHYASHRDH
NHRDETHGSS DHRHRESRHR SRDVDREQDH NECNKQRSRH KSKDRYCEKD GEVISKKRNE
AGEWNRDVYI RQ*
mutated AA sequence MKATWIRLLK RAKGGRLKNS DICGSADSYT SRPSDSDVSL EEDREAVRRE AERQAQAQLE
KAKTKPVAFA VRTNVSYSAA HEDDVPVPGM AISFEAKDFL HVKEKFNNDW WIGRLVKEGC
EIGFIPSPVK LENMRLQHEQ RAKQGKFYSS KSGGNSSSSL GDIVPSSRKS TPPSSAIDID
ATGLDAEEND IPANHRSPKP SANSVTSPHS KEKRMPFFKK TEHTPPYDVV PSMRPVVLVG
PSLKGYEVTD MMQKALFDFL KHRFEGRISI TRVTADISLA KRSVLNNPSK HAIIERSNTR
SSLAEVQSEI ERIFELARTL QLVVLDADTI NHPAQLSKTS LAPIIVYVKI SSPKVLQRLI
KSRGKSQAKH LNVQMVAADK LAQCPPELFD VILDENQLED ACEHLADYLE AYWKATHPPS
SSLPNPLLSR TLATSSLPLS PTLASNSQGS QGDQRTDRSA PIRSASQAEE EPSVEPVKKS
QHRSSSLAPH HNHRSGTSRG LSRQETFDSE TQESRDSAYV EPKEDYSHDH VDHYASHRDH
NHRDETHGSS DHRHRESRHR SRDVDREQDH NECNKQRSRH KSKDRYCEKD GEVISKKRNE
AGEWNRDVYI RQ*
speed 0.88 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