Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM092874)
  • known disease mutation: rs6504 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:103026205T>CN/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 intron
DNA changes g.46046T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs137853028
databasehomozygous (C/C)heterozygousallele carriers
1000G011
ExAC044

known disease mutation: rs6504 (pathogenic for Short-rib thoracic dysplasia 3 with or without polydactyly) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM092874)

known disease mutation at this position, please check HGMD for details (HGMD ID CM092874)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092874)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4710.996
5.0231
(flanking)1.3521
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased46050wt: 0.82 / mu: 0.97wt: ATTGTAGCCAAAGCT
mu: ACTGTAGCCAAAGCT		 TGTA|gcca
Donor increased46038wt: 0.23 / mu: 0.27wt: GTAGCTGATACAATT
mu: GTAGCTGATACAACT		 AGCT|gata
Donor marginally increased46040wt: 0.8525 / mu: 0.8623 (marginal change - not scored)wt: AGCTGATACAATTGT
mu: AGCTGATACAACTGT		 CTGA|taca
Donor increased46045wt: 0.60 / mu: 0.90wt: ATACAATTGTAGCCA
mu: ATACAACTGTAGCCA		 ACAA|ttgt
distance from splice site 21057
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
11650REGIONStem (By similarity).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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 46046
chromosomal position
(for ins/del: last normal base / first normal base)		 103026205
original gDNA sequence snippet GCTCAGAGTAGCTGATACAATTGTAGCCAAAGCTGCCGACC
altered gDNA sequence snippet GCTCAGAGTAGCTGATACAACTGTAGCCAAAGCTGCCGACC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.50 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