Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999975809 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:41903782A>CN/A show variant in all transcripts   IGV
HGNC symbol CCND3
Ensembl transcript ID ENST00000415497
Genbank transcript ID NM_001136126
UniProt peptide P30281
alteration type single base exchange
alteration region CDS
DNA changes c.187T>G
cDNA.755T>G
g.114314T>G
AA changes S63A Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 63
frameshift no
known variant Reference ID: rs1051130
databasehomozygous (C/C)heterozygousallele carriers
1000G93610952031
ExAC18016-326514751
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8750.144
-0.0330.003
(flanking)-1.7620
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased114318wt: 0.9237 / mu: 0.9307 (marginal change - not scored)wt: CTCTCAGACCAGCTC
mu: CGCTCAGACCAGCTC		 CTCA|gacc
Donor gained1143130.50mu: GAAGCCGCTCAGACC AGCC|gctc
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      63EAALRESLREASQTSSSPAPKAPR
mutated  all conserved    63EAAQTSSSPAPKAP
Ptroglodytes  no homologue    
Mmulatta  all conserved  ENSMMUG00000004419  259EAAQTSSSPAPKAP
Fcatus  all conserved  ENSFCAG00000004865  202EAAQTSPSPAPKAP
Mmusculus  all conserved  ENSMUSG00000034165  259EAAQTAPSPVPKAP
Ggallus  all identical  ENSGALG00000003485  261LKQASQSQQEYSTAKT
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0010315  81YASVDSAAKNPEQLEPPPPPPPP
Celegans  all identical  Y38F1A.5  303QRCMSTTPIYTSEDAEKTEPTPSAP
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
27152DOMAINCyclin N-terminal.lost
5470HELIXlost
7791HELIXmight get lost (downstream of altered splice site)
9698HELIXmight get lost (downstream of altered splice site)
99114HELIXmight get lost (downstream of altered splice site)
123127HELIXmight get lost (downstream of altered splice site)
128130TURNmight get lost (downstream of altered splice site)
134147HELIXmight get lost (downstream of altered splice site)
148150TURNmight get lost (downstream of altered splice site)
157160HELIXmight get lost (downstream of altered splice site)
161166HELIXmight get lost (downstream of altered splice site)
172174TURNmight get lost (downstream of altered splice site)
175191HELIXmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
200213HELIXmight get lost (downstream of altered splice site)
222233HELIXmight get lost (downstream of altered splice site)
237252HELIXmight get lost (downstream of altered splice site)
263263MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
279279MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 291 / 291
position (AA) of stopcodon in wt / mu AA sequence 97 / 97
position of stopcodon in wt / mu cDNA 859 / 859
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 569 / 569
chromosome 6
strand -1
last intron/exon boundary 692
theoretical NMD boundary in CDS 73
length of CDS 291
coding sequence (CDS) position 187
cDNA position
(for ins/del: last normal base / first normal base)		 755
gDNA position
(for ins/del: last normal base / first normal base)		 114314
chromosomal position
(for ins/del: last normal base / first normal base)		 41903782
original gDNA sequence snippet GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA
altered gDNA sequence snippet GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA
original cDNA sequence snippet GGGAGAGCCTCAGGGAAGCCTCTCAGACCAGCTCCAGCCCA
altered cDNA sequence snippet GGGAGAGCCTCAGGGAAGCCGCTCAGACCAGCTCCAGCCCA
wildtype AA sequence MYPPSMIATG SIGAAVQGLG ACSMSGDELT ELLAGITGTE VDCLRACQEQ IEAALRESLR
EASQTSSSPA PKAPRGSSSQ GPSQTSTPTD VTAIHL*
mutated AA sequence MYPPSMIATG SIGAAVQGLG ACSMSGDELT ELLAGITGTE VDCLRACQEQ IEAALRESLR
EAAQTSSSPA PKAPRGSSSQ GPSQTSTPTD VTAIHL*
speed 1.34 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project