Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998925092799146 (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) chr14:95884323G>AN/A show variant in all transcripts   IGV
HGNC symbol SYNE3
Ensembl transcript ID ENST00000554873
Genbank transcript ID N/A
UniProt peptide Q6ZMZ3
alteration type single base exchange
alteration region CDS
DNA changes c.2039C>T
cDNA.2444C>T
g.57851C>T
AA changes A680V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 680
frameshift no
known variant Reference ID: rs12434757
databasehomozygous (A/A)heterozygousallele carriers
1000G76712211988
ExAC23457-141479310
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3150.995
0.5890.996
(flanking)5.5840.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc gained578490.35mu: CTGGGCTCCCTCTTCCGGAGGGTGTGCTGTGTGGCGCTCCC gagg|GTGT
Donor gained578440.76mu: TCTTCCGGAGGGTGT TTCC|ggag
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      680RWRGLGSLFRRACCVALPLQLLLL
mutated  not conserved    680RWRGLGSLFRRVCCVALPLQLLL
Ptroglodytes  not conserved  ENSPTRG00000006691  898LFRRVCCVALPLQLLL
Mmulatta  not conserved  ENSMMUG00000004931  923LFRRVCCVALPLQLLL
Fcatus  not conserved  ENSFCAG00000012093  908LFRKVCCVALPLQLLF
Mmusculus  all identical  ENSMUSG00000054150  922CSLLQKACRVALPLQLLL
Ggallus  not conserved  ENSGALG00000011076  906CSFLHRVCWASLPLQLLL
Trubripes  not conserved  ENSTRUG00000005974  935------SLLQRVCRLALPLWLLL
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000023311  927GGLCSFLHRVCCAALPLQLLL
protein features
start (aa)end (aa)featuredetails 
1925TOPO_DOMCytoplasmic (Potential).lost
647740REPEATSpectrin 2.lost
917975DOMAINKASH.might get lost (downstream of altered splice site)
926946TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
947975TOPO_DOMPerinuclear space (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2199 / 2199
position (AA) of stopcodon in wt / mu AA sequence 733 / 733
position of stopcodon in wt / mu cDNA 2604 / 2604
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 406 / 406
chromosome 14
strand -1
last intron/exon boundary 2404
theoretical NMD boundary in CDS 1948
length of CDS 2199
coding sequence (CDS) position 2039
cDNA position
(for ins/del: last normal base / first normal base)		 2444
gDNA position
(for ins/del: last normal base / first normal base)		 57851
chromosomal position
(for ins/del: last normal base / first normal base)		 95884323
original gDNA sequence snippet GGGCTCCCTCTTCCGGAGGGCGTGCTGTGTGGCGCTCCCAC
altered gDNA sequence snippet GGGCTCCCTCTTCCGGAGGGTGTGCTGTGTGGCGCTCCCAC
original cDNA sequence snippet GGGCTCCCTCTTCCGGAGGGCGTGCTGTGTGGCGCTCCCAC
altered cDNA sequence snippet GGGCTCCCTCTTCCGGAGGGTGTGCTGTGTGGCGCTCCCAC
wildtype AA sequence MQQLYSFSLP VFPSPLYPLQ DIAKDFPRGE ESLETLEEQS AGVIRNTSPL GAEKITGELE
EMRKVLEKLR ALWEEEEERL RGLLRSRGAW EQQIKQLEAE LSEFRMVLQR LAQEGLQPAA
KAGTEDELVA HWRRYSATRA ALASEEPRVD RLQAQLKELI VFPHNLKPLS DSVIATIQEY
QSLKVKSARL RNAAAVELWQ HFQRPLQDLQ LWKALAQRLL EVTASLPDLP SLHTFLPQIE
AALMESSRLK ELLTMLQLKK DLLIGIFGQE RATALLEQVA GSMRDRDLLH NSLLQRKSKL
QSLLAQHKDF GAAFEPLQRK LLDLQVRVQA EKGLQRDLPG KQAQLSRLQG LQEEGLDLGA
QMEAARPLVQ ENPNHQHKMD QLSSDFQALQ RSLEDLVDRC RQSVQEHCTF SHQLLELRQW
IVVTTQKLEA HRGEAGPGDA ESQEAEFERL VAEFPEKEAQ LSLVEAQGWL VMEKSSPEGA
AVVQEELREL AESWRALRLL EESLLSLIRN WHLQRMEVDS GKKMVFTNNI PKSGFLINPM
DPIPRHRRRA NLLQEEEGSH EDFSQLLRNF GQWLQVENSK LVRIIAMRTS TAEDLRTRKS
KLQELEARVP EGQHLFENLL RLGPARGTSD ELEDLRYQWM LYKSKLKDSG HLLTQSSPGE
PTGFQKTRRW RGLGSLFRRA CCVALPLQLL LLLFLLLLFL LPIREEDRSC TLANNFARSF
TLMLRYNGPP PT*
mutated AA sequence MQQLYSFSLP VFPSPLYPLQ DIAKDFPRGE ESLETLEEQS AGVIRNTSPL GAEKITGELE
EMRKVLEKLR ALWEEEEERL RGLLRSRGAW EQQIKQLEAE LSEFRMVLQR LAQEGLQPAA
KAGTEDELVA HWRRYSATRA ALASEEPRVD RLQAQLKELI VFPHNLKPLS DSVIATIQEY
QSLKVKSARL RNAAAVELWQ HFQRPLQDLQ LWKALAQRLL EVTASLPDLP SLHTFLPQIE
AALMESSRLK ELLTMLQLKK DLLIGIFGQE RATALLEQVA GSMRDRDLLH NSLLQRKSKL
QSLLAQHKDF GAAFEPLQRK LLDLQVRVQA EKGLQRDLPG KQAQLSRLQG LQEEGLDLGA
QMEAARPLVQ ENPNHQHKMD QLSSDFQALQ RSLEDLVDRC RQSVQEHCTF SHQLLELRQW
IVVTTQKLEA HRGEAGPGDA ESQEAEFERL VAEFPEKEAQ LSLVEAQGWL VMEKSSPEGA
AVVQEELREL AESWRALRLL EESLLSLIRN WHLQRMEVDS GKKMVFTNNI PKSGFLINPM
DPIPRHRRRA NLLQEEEGSH EDFSQLLRNF GQWLQVENSK LVRIIAMRTS TAEDLRTRKS
KLQELEARVP EGQHLFENLL RLGPARGTSD ELEDLRYQWM LYKSKLKDSG HLLTQSSPGE
PTGFQKTRRW RGLGSLFRRV CCVALPLQLL LLLFLLLLFL LPIREEDRSC TLANNFARSF
TLMLRYNGPP PT*
speed 1.17 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