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 marginally increased398674wt: 0.7808 / mu: 0.8361 (marginal change - not scored)wt: ACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGT
mu: ACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGT		 gccc|CACA
Acc increased398668wt: 0.33 / mu: 0.42wt: CCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCAT
mu: CCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCAT		 tcct|CAGC
Acc marginally increased398667wt: 0.8987 / mu: 0.9546 (marginal change - not scored)wt: TCCCAGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCA
mu: TCCCAGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCA		 ctcc|TCAG
Acc marginally increased398671wt: 0.8411 / mu: 0.9178 (marginal change - not scored)wt: AGCACCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGC
mu: AGCACCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGC		 tcag|CCCC
Acc increased398675wt: 0.39 / mu: 0.57wt: CCGCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTG
mu: CCGCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTG		 cccc|ACAC
Acc increased398679wt: 0.78 / mu: 0.89wt: TCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGGAC
mu: TCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGGAC		 acac|CACA
Acc marginally increased398677wt: 0.8363 / mu: 0.8908 (marginal change - not scored)wt: GCTCTTCCTCCTCAGCCCCACACCACAACCATCGCAGTGGG
mu: GCTCTTCCTCCTTAGCCCCACACCACAACCATCGCAGTGGG		 ccac|ACCA
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 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