Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999984250595168 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001137)
  • known disease mutation: rs16674 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130582213C>AN/A show variant in all transcripts   IGV
HGNC symbol ENG
Ensembl transcript ID ENST00000373203
Genbank transcript ID NM_001114753
UniProt peptide P17813
alteration type single base exchange
alteration region CDS
DNA changes c.1238G>T
cDNA.1639G>T
g.34823G>T
AA changes G413V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 413
frameshift no
known variant Reference ID: rs121918401
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16674 (pathogenic for Hereditary hemorrhagic telangiectasia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001137)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001137)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001137)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5081
2.7411
(flanking)2.7410.997
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 increased34816wt: 0.9828 / mu: 0.9899 (marginal change - not scored)wt: ACTCCAGCTGTGGCA
mu: ACTCCAGCTGTGTCA		 TCCA|gctg
Donor increased34821wt: 0.62 / mu: 0.88wt: AGCTGTGGCATGCAG
mu: AGCTGTGTCATGCAG		 CTGT|ggca
Donor increased34825wt: 0.49 / mu: 0.64wt: GTGGCATGCAGGTGT
mu: GTGTCATGCAGGTGT		 GGCA|tgca
Acc gained348280.33mu: CTTACTCCAGCTGTGTCATGCAGGTGTCAGCAAGTATGATC atgc|AGGT
Acc gained348300.32mu: TACTCCAGCTGTGTCATGCAGGTGTCAGCAAGTATGATCAG gcag|GTGT
distance from splice site 35
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      413KFVLRSAYSSCGMQVSASMISNEA
mutated  not conserved    413KFVLRSAYSSCVMQVSASM
Ptroglodytes  all identical  ENSPTRG00000021400  288KFVLRSAYSSCGMQVSASMISNE
Mmulatta  all identical  ENSMMUG00000002248  141QFVLHSAYSSCGMEVTANMISNE
Fcatus  not conserved  ENSFCAG00000001489  411XXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000026814  413HLVLSSAYSSCGMKVTA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
26586TOPO_DOMExtracellular (Potential).lost
336576COMPBIASSer/Thr-rich.lost
587611TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
612658TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
646646MOD_RESPhosphoserine; by TGFBR1 (By similarity).might get lost (downstream of altered splice site)
649649MOD_RESPhosphoserine; by TGFBR1 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1977 / 1977
position (AA) of stopcodon in wt / mu AA sequence 659 / 659
position of stopcodon in wt / mu cDNA 2378 / 2378
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 402 / 402
chromosome 9
strand -1
last intron/exon boundary 2254
theoretical NMD boundary in CDS 1802
length of CDS 1977
coding sequence (CDS) position 1238
cDNA position
(for ins/del: last normal base / first normal base)		 1639
gDNA position
(for ins/del: last normal base / first normal base)		 34823
chromosomal position
(for ins/del: last normal base / first normal base)		 130582213
original gDNA sequence snippet CAGTGCTTACTCCAGCTGTGGCATGCAGGTGTCAGCAAGTA
altered gDNA sequence snippet CAGTGCTTACTCCAGCTGTGTCATGCAGGTGTCAGCAAGTA
original cDNA sequence snippet CAGTGCTTACTCCAGCTGTGGCATGCAGGTGTCAGCAAGTA
altered cDNA sequence snippet CAGTGCTTACTCCAGCTGTGTCATGCAGGTGTCAGCAAGTA
wildtype AA sequence MDRGTLPLAV ALLLASCSLS PTSLAETVHC DLQPVGPERG EVTYTTSQVS KGCVAQAPNA
ILEVHVLFLE FPTGPSQLEL TLQASKQNGT WPREVLLVLS VNSSVFLHLQ ALGIPLHLAY
NSSLVTFQEP PGVNTTELPS FPKTQILEWA AERGPITSAA ELNDPQSILL RLGQAQGSLS
FCMLEASQDM GRTLEWRPRT PALVRGCHLE GVAGHKEAHI LRVLPGHSAG PRTVTVKVEL
SCAPGDLDAV LILQGPPYVS WLIDANHNMQ IWTTGEYSFK IFPEKNIRGF KLPDTPQGLL
GEARMLNASI VASFVELPLA SIVSLHASSC GGRLQTSPAP IQTTPPKDTC SPELLMSLIQ
TKCADDAMTL VLKKELVAHL KCTITGLTFW DPSCEAEDRG DKFVLRSAYS SCGMQVSASM
ISNEAVVNIL SSSSPQRKKV HCLNMDSLSF QLGLYLSPHF LQASNTIEPG QQSFVQVRVS
PSVSEFLLQL DSCHLDLGPE GGTVELIQGR AAKGNCVSLL SPSPEGDPRF SFLLHFYTVP
IPKTGTLSCT VALRPKTGSQ DQEVHRTVFM RLNIISPDLS GCTSKGLVLP AVLGITFGAF
LIGALLTAAL WYIYSHTRSP SKREPVVAVA APASSESSST NHSIGSTQST PCSTSSMA*
mutated AA sequence MDRGTLPLAV ALLLASCSLS PTSLAETVHC DLQPVGPERG EVTYTTSQVS KGCVAQAPNA
ILEVHVLFLE FPTGPSQLEL TLQASKQNGT WPREVLLVLS VNSSVFLHLQ ALGIPLHLAY
NSSLVTFQEP PGVNTTELPS FPKTQILEWA AERGPITSAA ELNDPQSILL RLGQAQGSLS
FCMLEASQDM GRTLEWRPRT PALVRGCHLE GVAGHKEAHI LRVLPGHSAG PRTVTVKVEL
SCAPGDLDAV LILQGPPYVS WLIDANHNMQ IWTTGEYSFK IFPEKNIRGF KLPDTPQGLL
GEARMLNASI VASFVELPLA SIVSLHASSC GGRLQTSPAP IQTTPPKDTC SPELLMSLIQ
TKCADDAMTL VLKKELVAHL KCTITGLTFW DPSCEAEDRG DKFVLRSAYS SCVMQVSASM
ISNEAVVNIL SSSSPQRKKV HCLNMDSLSF QLGLYLSPHF LQASNTIEPG QQSFVQVRVS
PSVSEFLLQL DSCHLDLGPE GGTVELIQGR AAKGNCVSLL SPSPEGDPRF SFLLHFYTVP
IPKTGTLSCT VALRPKTGSQ DQEVHRTVFM RLNIISPDLS GCTSKGLVLP AVLGITFGAF
LIGALLTAAL WYIYSHTRSP SKREPVVAVA APASSESSST NHSIGSTQST PCSTSSMA*
speed 1.25 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