Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998543854 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM091949)
  • known disease mutation: rs6506 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:102995926C>TN/A show variant in all transcripts   IGV
HGNC symbol DYNC2H1
Ensembl transcript ID ENST00000334267
Genbank transcript ID N/A
UniProt peptide Q8NCM8
alteration type single base exchange
alteration region CDS
DNA changes c.1759C>T
cDNA.1812C>T
g.15767C>T
AA changes R587C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 587
frameshift no
known variant Reference ID: rs137853030
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs6506 (pathogenic for Short-rib thoracic dysplasia 3 with or without polydactyly|Short-rib polydactyly syndrome type III) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM091949)

known disease mutation at this position, please check HGMD for details (HGMD ID CM091949)
known disease mutation at this position, please check HGMD for details (HGMD ID CM091949)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8110.767
3.6761
(flanking)5.6851
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 increased15760wt: 0.4727 / mu: 0.4781 (marginal change - not scored)wt: CGTTTGGTGATTCTTCTGAGAGAAGTTCGTCAGCTCTCTGC
mu: CGTTTGGTGATTCTTCTGAGAGAAGTTTGTCAGCTCTCTGC		 gaga|GAAG
Acc increased15757wt: 0.23 / mu: 0.33wt: GATCGTTTGGTGATTCTTCTGAGAGAAGTTCGTCAGCTCTC
mu: GATCGTTTGGTGATTCTTCTGAGAGAAGTTTGTCAGCTCTC		 tctg|AGAG
Donor marginally increased15758wt: 0.9987 / mu: 0.9988 (marginal change - not scored)wt: TTCTGAGAGAAGTTC
mu: TTCTGAGAGAAGTTT		 CTGA|gaga
distance from splice site 98
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      587SDRLVILLREVRQLSALGFVIPAK
mutated  not conserved    587SDRLVILLREVCQLSALGFVIPA
Ptroglodytes  all identical  ENSPTRG00000004224  587SDRLVILLREVRQLSALGFVIPA
Mmulatta  no alignment  ENSMMUG00000018308  n/a
Fcatus  no alignment  ENSFCAG00000000121  n/a
Mmusculus  all identical  ENSMUSG00000047193  587SDRLVILLREVRQLSALGFVIPA
Ggallus  all identical  ENSGALG00000017180  585SDRLVTLLREVRQLSALGFVIPA
Trubripes  all identical  ENSTRUG00000004354  585SDRLGSLVREVRQLTALGFTV
Drerio  no alignment  ENSDARG00000090725  n/a
Dmelanogaster  all identical  FBgn0023096  555NPKLVTFCQDVREFENL
Celegans  all identical  F18C12.1  547SDRLLRLLKEVRQLISLGFN
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
11650REGIONStem (By similarity).lost
594594CONFLICTF -> L (in Ref. 1; BAE17138).might get lost (downstream of altered splice site)
10741103COILEDPotential.might get lost (downstream of altered splice site)
11201120CONFLICTI -> N (in Ref. 4; AAB09728).might get lost (downstream of altered splice site)
11681168CONFLICTD -> V (in Ref. 4; AAB09728).might get lost (downstream of altered splice site)
16511875REGIONAAA 1 (By similarity).might get lost (downstream of altered splice site)
16891696NP_BINDATP (Potential).might get lost (downstream of altered splice site)
17841784CONFLICTN -> H (in Ref. 6; CAB06054).might get lost (downstream of altered splice site)
18641864CONFLICTW -> Y (in Ref. 6; CAB06054).might get lost (downstream of altered splice site)
18661867CONFLICTLR -> FS (in Ref. 6; CAB06054).might get lost (downstream of altered splice site)
19301930CONFLICTE -> K (in Ref. 1; BAE46899).might get lost (downstream of altered splice site)
19382161REGIONAAA 2 (By similarity).might get lost (downstream of altered splice site)
19791986NP_BINDATP (Potential).might get lost (downstream of altered splice site)
22512505REGIONAAA 3 (By similarity).might get lost (downstream of altered splice site)
22912298NP_BINDATP (Potential).might get lost (downstream of altered splice site)
26172863REGIONAAA 4 (By similarity).might get lost (downstream of altered splice site)
26552662NP_BINDATP (Potential).might get lost (downstream of altered splice site)
28813169REGIONStalk (By similarity).might get lost (downstream of altered splice site)
28972982COILEDPotential.might get lost (downstream of altered splice site)
30953095CONFLICTA -> V (in Ref. 7; CAD98012).might get lost (downstream of altered splice site)
31093200COILEDPotential.might get lost (downstream of altered splice site)
32443473REGIONAAA 5 (By similarity).might get lost (downstream of altered splice site)
34083442COILEDPotential.might get lost (downstream of altered splice site)
36653665CONFLICTL -> P (in Ref. 7; CAD98012).might get lost (downstream of altered splice site)
36903905REGIONAAA 6 (By similarity).might get lost (downstream of altered splice site)
42584258CONFLICTC -> R (in Ref. 3; BAB13905).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2763 / 2763
position (AA) of stopcodon in wt / mu AA sequence 921 / 921
position of stopcodon in wt / mu cDNA 2816 / 2816
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 54 / 54
chromosome 11
strand 1
last intron/exon boundary 2658
theoretical NMD boundary in CDS 2554
length of CDS 2763
coding sequence (CDS) position 1759
cDNA position
(for ins/del: last normal base / first normal base)		 1812
gDNA position
(for ins/del: last normal base / first normal base)		 15767
chromosomal position
(for ins/del: last normal base / first normal base)		 102995926
original gDNA sequence snippet TGATTCTTCTGAGAGAAGTTCGTCAGCTCTCTGCACTTGGC
altered gDNA sequence snippet TGATTCTTCTGAGAGAAGTTTGTCAGCTCTCTGCACTTGGC
original cDNA sequence snippet TGATTCTTCTGAGAGAAGTTCGTCAGCTCTCTGCACTTGGC
altered cDNA sequence snippet TGATTCTTCTGAGAGAAGTTTGTCAGCTCTCTGCACTTGGC
wildtype AA sequence MANGTADVRK LFIFTTTQNY FGLMSELWDQ PLLCNCLEIN NFLDDGNQML LRVQRSDAGI
SFSNTIEFGD TKDKVLVFFK LRPEVITDEN LHDNILVSSM LESPISSLYQ AVRQVFAPML
LKDQEWSRNF DPKLQNLLSE LEAGLGIVLR RSDTNLTKLK FKEDDTRGIL TPSDEFQFWI
EQAHRGNKQI SKERANYFKE LFETIAREFY NLDSLSLLEV VDLVETTQDV VDDVWRQTEH
DHYPESRMLH LLDIIGGSFG RFVQKKLGTL NLWEDPYYLV KESLKAGISI CEQWVIVCNH
LTGQVWQRYV PHPWKNEKYF PETLDKLGKR LEEVLAIRTI HEKFLYFLPA SEEKIICLTR
VFEPFTGLNP VQYNPYTEPL WKAAVSQYEK IIAPAEQKIA GKLKNYISEI QDSPQQLLQA
FLKYKELVKR PTISKELMLE RETLLARLVD SIKDFRLDFE NRCRGIPGDA SGPLSGKNLS
EVVNSIVWVR QLELKVDDTI KIAEALLSDL PGFRCFHQSA KDLLDQLKLY EQEQFDDWSR
DIQSGLSDSR SGLCIEASSR IMELDSNDGL LKVHYSDRLV ILLREVRQLS ALGFVIPAKI
QQVANIAQKF CKQAIILKQV AHFYNSIDQQ MIQSQRPMML QSALAFEQII KNSKAGSGGK
SQITWDNPKE LEGYIQKLQN AAERLATENR KLRKWHTTFC EKVVVLMNID LLRQQQRWKD
GLQELRTGLA TVEAQCPLAW QSKWEGPEDP LQYLRGLVAR ALAIQNWVDK AEKQALLSET
LDLSELFHPD TFLNALRQET ARAVGRSVDS LKFVASWKGR LQEAKLQIKI SGLLLEGCSF
DGNQLSENQL DSPSVSSVLP CFMGWIPQDA CGPYSPDECI SLPVYTSAER DRVVTNIDVP
CGGNQDQWIQ CGAALFLKNQ *
mutated AA sequence MANGTADVRK LFIFTTTQNY FGLMSELWDQ PLLCNCLEIN NFLDDGNQML LRVQRSDAGI
SFSNTIEFGD TKDKVLVFFK LRPEVITDEN LHDNILVSSM LESPISSLYQ AVRQVFAPML
LKDQEWSRNF DPKLQNLLSE LEAGLGIVLR RSDTNLTKLK FKEDDTRGIL TPSDEFQFWI
EQAHRGNKQI SKERANYFKE LFETIAREFY NLDSLSLLEV VDLVETTQDV VDDVWRQTEH
DHYPESRMLH LLDIIGGSFG RFVQKKLGTL NLWEDPYYLV KESLKAGISI CEQWVIVCNH
LTGQVWQRYV PHPWKNEKYF PETLDKLGKR LEEVLAIRTI HEKFLYFLPA SEEKIICLTR
VFEPFTGLNP VQYNPYTEPL WKAAVSQYEK IIAPAEQKIA GKLKNYISEI QDSPQQLLQA
FLKYKELVKR PTISKELMLE RETLLARLVD SIKDFRLDFE NRCRGIPGDA SGPLSGKNLS
EVVNSIVWVR QLELKVDDTI KIAEALLSDL PGFRCFHQSA KDLLDQLKLY EQEQFDDWSR
DIQSGLSDSR SGLCIEASSR IMELDSNDGL LKVHYSDRLV ILLREVCQLS ALGFVIPAKI
QQVANIAQKF CKQAIILKQV AHFYNSIDQQ MIQSQRPMML QSALAFEQII KNSKAGSGGK
SQITWDNPKE LEGYIQKLQN AAERLATENR KLRKWHTTFC EKVVVLMNID LLRQQQRWKD
GLQELRTGLA TVEAQCPLAW QSKWEGPEDP LQYLRGLVAR ALAIQNWVDK AEKQALLSET
LDLSELFHPD TFLNALRQET ARAVGRSVDS LKFVASWKGR LQEAKLQIKI SGLLLEGCSF
DGNQLSENQL DSPSVSSVLP CFMGWIPQDA CGPYSPDECI SLPVYTSAER DRVVTNIDVP
CGGNQDQWIQ CGAALFLKNQ *
speed 1.04 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