Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.85299986174086 (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 CM054795)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:32453358G>AN/A show variant in all transcripts   IGV
HGNC symbol NRG1
Ensembl transcript ID ENST00000520407
Genbank transcript ID NM_013962
UniProt peptide Q02297
alteration type single base exchange
alteration region CDS
DNA changes c.758G>A
cDNA.988G>A
g.956457G>A
AA changes R253Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 253
frameshift no
known variant Reference ID: rs3924999
databasehomozygous (A/A)heterozygousallele carriers
1000G5318671398
ExAC104161193522351

known disease mutation at this position, please check HGMD for details (HGMD ID CM054795)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8950.982
2.2861
(flanking)0.7321
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 increased956448wt: 0.9609 / mu: 0.9706 (marginal change - not scored)wt: CTCTTTTCTTCTTTTAGCCTTGCCTCCCCGATTGAAAGAGA
mu: CTCTTTTCTTCTTTTAGCCTTGCCTCCCCAATTGAAAGAGA		 cctt|GCCT
Acc increased956460wt: 0.61 / mu: 0.77wt: TTTAGCCTTGCCTCCCCGATTGAAAGAGATGAAAAGCCAGG
mu: TTTAGCCTTGCCTCCCCAATTGAAAGAGATGAAAAGCCAGG		 gatt|GAAA
Acc marginally increased956457wt: 0.9581 / mu: 0.9697 (marginal change - not scored)wt: TCTTTTAGCCTTGCCTCCCCGATTGAAAGAGATGAAAAGCC
mu: TCTTTTAGCCTTGCCTCCCCAATTGAAAGAGATGAAAAGCC		 cccg|ATTG
Acc marginally increased956452wt: 0.8266 / mu: 0.8304 (marginal change - not scored)wt: TTTCTTCTTTTAGCCTTGCCTCCCCGATTGAAAGAGATGAA
mu: TTTCTTCTTTTAGCCTTGCCTCCCCAATTGAAAGAGATGAA		 gcct|CCCC
Donor increased956459wt: 0.56 / mu: 0.86wt: CCCGATTGAAAGAGA
mu: CCCAATTGAAAGAGA		 CGAT|tgaa
Donor increased956458wt: 0.72 / mu: 0.87wt: CCCCGATTGAAAGAG
mu: CCCCAATTGAAAGAG		 CCGA|ttga
Donor gained9564530.43mu: TGCCTCCCCAATTGA CCTC|ccca
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      253RVLCKRCALPPRLKEMKSQESAAG
mutated  all conserved    253RVLCKRCALPPQLKEMKSQESAA
Ptroglodytes  all identical  ENSPTRG00000020146  38AAGSQSPALPPRLKEMKSQESAA
Mmulatta  all identical  ENSMMUG00000000208  38ALPPRLKEMKSQESAA
Fcatus  all identical  ENSFCAG00000014970  4LPPRLKEMRSQESVA
Mmusculus  no alignment  ENSMUSG00000062991  n/a
Ggallus  no alignment  ENSGALG00000015422  n/a
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000068458  168QVLCQDCA-EPKLKNLRSVTVED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000017504  n/a
protein features
start (aa)end (aa)featuredetails 
243265TRANSMEMHelical; Note=Internal signal sequence; (Potential).lost
261261CONFLICTV -> L (in Ref. 9; ABQ53540).might get lost (downstream of altered splice site)
266640TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
414414CONFLICTS -> F (in Ref. 2; AAA19953).might get lost (downstream of altered splice site)
535535CONFLICTQ -> R (in Ref. 2; AAA19951).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1269 / 1269
position (AA) of stopcodon in wt / mu AA sequence 423 / 423
position of stopcodon in wt / mu cDNA 1499 / 1499
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 231 / 231
chromosome 8
strand 1
last intron/exon boundary 1406
theoretical NMD boundary in CDS 1125
length of CDS 1269
coding sequence (CDS) position 758
cDNA position
(for ins/del: last normal base / first normal base)		 988
gDNA position
(for ins/del: last normal base / first normal base)		 956457
chromosomal position
(for ins/del: last normal base / first normal base)		 32453358
original gDNA sequence snippet TCTTTTAGCCTTGCCTCCCCGATTGAAAGAGATGAAAAGCC
altered gDNA sequence snippet TCTTTTAGCCTTGCCTCCCCAATTGAAAGAGATGAAAAGCC
original cDNA sequence snippet GCGGTGCGCCTTGCCTCCCCGATTGAAAGAGATGAAAAGCC
altered cDNA sequence snippet GCGGTGCGCCTTGCCTCCCCAATTGAAAGAGATGAAAAGCC
wildtype AA sequence MRWRRAPRRS GRPGPRAQRP GSAARSSPPL PLLPLLLLLG TAALAPGAAA GNEAAPAGAS
VCYSSPPSVG SVQELAQRAA VVIEGKVHPQ RRQQGALDRK AAAAAGEAGA WGGDREPPAA
GPRALGPPAE EPLLAANGTV PSWPTAPVPS AGEPGEEAPY LVKVHQVWAV KAGGLKKDSL
LTVRLGTWGH PAFPSCGRLK EDSRYIFFME PDANSTSRAP AAFRASFPPL ETGRNLKKEV
SRVLCKRCAL PPRLKEMKSQ ESAAGSKLVL RCETSSEYSS LRFKWFKNGN ELNRKNKPQN
IKIQKKPGKS ELRINKASLA DSGEYMCKVI SKLGNDSASA NITIVESNAT STSTTGTSHL
VKCAEKEKTF CVNGGECFMV KDLSNPSRYL CKCPNEFTGD RCQNYVMASF YSTSTPFLSL
PE*
mutated AA sequence MRWRRAPRRS GRPGPRAQRP GSAARSSPPL PLLPLLLLLG TAALAPGAAA GNEAAPAGAS
VCYSSPPSVG SVQELAQRAA VVIEGKVHPQ RRQQGALDRK AAAAAGEAGA WGGDREPPAA
GPRALGPPAE EPLLAANGTV PSWPTAPVPS AGEPGEEAPY LVKVHQVWAV KAGGLKKDSL
LTVRLGTWGH PAFPSCGRLK EDSRYIFFME PDANSTSRAP AAFRASFPPL ETGRNLKKEV
SRVLCKRCAL PPQLKEMKSQ ESAAGSKLVL RCETSSEYSS LRFKWFKNGN ELNRKNKPQN
IKIQKKPGKS ELRINKASLA DSGEYMCKVI SKLGNDSASA NITIVESNAT STSTTGTSHL
VKCAEKEKTF CVNGGECFMV KDLSNPSRYL CKCPNEFTGD RCQNYVMASF YSTSTPFLSL
PE*
speed 1.07 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