Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.962488327806802 (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) chr2:136393658A>GN/A show variant in all transcripts   IGV
HGNC symbol R3HDM1
Ensembl transcript ID ENST00000409478
Genbank transcript ID N/A
UniProt peptide Q15032
alteration type single base exchange
alteration region CDS
DNA changes c.676A>G
cDNA.1058A>G
g.104634A>G
AA changes M226V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 226
frameshift no
known variant Reference ID: rs961360
databasehomozygous (G/G)heterozygousallele carriers
1000G26610171283
ExAC43922029424686
regulatory features H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7351
3.1131
(flanking)3.4491
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost104633sequence motif lost- wt: gtag|ATGA
 mu: gtag.GTGA
Acc increased104630wt: 0.45 / mu: 0.57wt: TAAAAATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAA
mu: TAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAA		 tctg|TAGA
Acc gained1046260.33mu: TGCCTAAAAATTATCCTCTTTTCTGTAGGTGAGAATACGTT cttt|TCTG
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      226DNSSFDKDDNQMRIRLKDDRRSKS
mutated  all conserved    226DNSSFDKDDNQVRIRLKDDRRSK
Ptroglodytes  not conserved  ENSPTRG00000012494  270DRRSKSIEEREEEYQRARDRIFSQ
Mmulatta  not conserved  ENSMMUG00000009844  214DNSSFDKDDNQ-----------
Fcatus  no alignment  ENSFCAG00000019217  n/a
Mmusculus  not conserved  ENSMUSG00000056211  270DRRSKSIEEREEEYQRARDRIFS
Ggallus  all identical  ENSGALG00000012246  270DNSSLDKDDNQMRIRLKDDRRSK
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000063141  211DNSSLDQDDGRLRMRLK
Dmelanogaster  not conserved  FBgn0004875  543DTHSFDEVRQSPYLCPLSLDRKAK
Celegans  no alignment  ZK121.2  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
168231DOMAINR3H.lost
251301DOMAINSUZ.might get lost (downstream of altered splice site)
337337MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
381381MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
541541CONFLICTQ -> QQ (in Ref. 2; BAA04878).might get lost (downstream of altered splice site)
589608COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
822826COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
973973MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2916 / 2916
position (AA) of stopcodon in wt / mu AA sequence 972 / 972
position of stopcodon in wt / mu cDNA 3298 / 3298
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 383 / 383
chromosome 2
strand 1
last intron/exon boundary 2943
theoretical NMD boundary in CDS 2510
length of CDS 2916
coding sequence (CDS) position 676
cDNA position
(for ins/del: last normal base / first normal base)		 1058
gDNA position
(for ins/del: last normal base / first normal base)		 104634
chromosomal position
(for ins/del: last normal base / first normal base)		 136393658
original gDNA sequence snippet AATTATCCTCTTTTCTGTAGATGAGAATACGTTTGAAAGAT
altered gDNA sequence snippet AATTATCCTCTTTTCTGTAGGTGAGAATACGTTTGAAAGAT
original cDNA sequence snippet TTGACAAAGATGATAACCAGATGAGAATACGTTTGAAAGAT
altered cDNA sequence snippet TTGACAAAGATGATAACCAGGTGAGAATACGTTTGAAAGAT
wildtype AA sequence MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQMRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQQDNLGSQF
SHMSLARQPS ADGSDPHAAM FQSTVVLQSP QQSGYIMTAA PPPHPPPPPP PPPPPPPLPP
GQPVPTAGYP ASGHPVSQPV LQQQGYIQQP SPQMPACYCA PGHYHSSQPQ YRPVPSVHYN
SHLNQPLPQP AQQTGYQVIP NQQQNYQGIV GVQQPQSQSL VSGQPNSIGN QIQGVVIPYT
SVPTYQVSLP QGSQGIPHQT YQQPVMFPNQ SNQGSMPTTG MPVYYSVIPP GQQNNLSSSV
GYLQHPGSEQ VQFPRTTSPC SSQQLQGHQC TAGPPPPPGG GMVMMQLSVP NNPQSCAHSP
PQWKQNKYYC DHQRGQKCVE FSSVDNIVQH SPQLSSPIIS PAQSPAPAQL STLKTVRPSG
PPLSIMPQFS RPFVPGQGDS RYPLLGQPLQ YNPPAVLHGH IPNQQGQPGS RHGNRGRRQA
KKAASTDLGA GETVVGKVLE ITELPDGITR MEAEKLFGEL FKIGAKIRWL RDPQSQPRRH
PLCCGSGDNT ANPERSKPSD LASTYTVLAT FPSISAAQNA LKKQINSVNK FKLRTSKKHY
DFHILERASS Q*
mutated AA sequence MRMSDTVTVK DETATMKDLE AEVKDTTRVE NLIKSENYGK ILVEKNEHCI ENNIDLQEKI
QIQLTQSFEK EEKPSKDEAE KEKASDKLPR KMLSRDSSQE YTDSTGIDLH EFLVNTLKNN
PRDRMMLLKL EQEILDFIGN NESPRKKFPP MTSYHRMLLH RVAAYFGLDH NVDQSGKSVI
VNKTSNTRIP DQKFNEHIKD DKGEDFQKRY ILKRDNSSFD KDDNQVRIRL KDDRRSKSIE
EREEEYQRAR DRIFSQDSLC SQENYIIDKR LQDEDASSTQ QRRQIFRVNK DASGRSTNSH
QSSTENELKY SEPRPWSSTD SDSSLRNLKP AVTKASSFSG ISVLTRGDSS GSSKSIGRLS
KTGQPFINPD GSPVVYNPPM TQQPVRSQVP GPPQPPLPAP PQQPAANHIF SQQDNLGSQF
SHMSLARQPS ADGSDPHAAM FQSTVVLQSP QQSGYIMTAA PPPHPPPPPP PPPPPPPLPP
GQPVPTAGYP ASGHPVSQPV LQQQGYIQQP SPQMPACYCA PGHYHSSQPQ YRPVPSVHYN
SHLNQPLPQP AQQTGYQVIP NQQQNYQGIV GVQQPQSQSL VSGQPNSIGN QIQGVVIPYT
SVPTYQVSLP QGSQGIPHQT YQQPVMFPNQ SNQGSMPTTG MPVYYSVIPP GQQNNLSSSV
GYLQHPGSEQ VQFPRTTSPC SSQQLQGHQC TAGPPPPPGG GMVMMQLSVP NNPQSCAHSP
PQWKQNKYYC DHQRGQKCVE FSSVDNIVQH SPQLSSPIIS PAQSPAPAQL STLKTVRPSG
PPLSIMPQFS RPFVPGQGDS RYPLLGQPLQ YNPPAVLHGH IPNQQGQPGS RHGNRGRRQA
KKAASTDLGA GETVVGKVLE ITELPDGITR MEAEKLFGEL FKIGAKIRWL RDPQSQPRRH
PLCCGSGDNT ANPERSKPSD LASTYTVLAT FPSISAAQNA LKKQINSVNK FKLRTSKKHY
DFHILERASS Q*
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