Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999983212 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM021270)
  • known disease mutation: rs8381 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:34021891A>GN/A show variant in all transcripts   IGV
HGNC symbol GDF5
Ensembl transcript ID ENST00000374369
Genbank transcript ID NM_000557
UniProt peptide P43026
alteration type single base exchange
alteration region CDS
DNA changes c.1322T>C
cDNA.1637T>C
g.20678T>C
AA changes L441P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 441
frameshift no
known variant Reference ID: rs28936683
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8381 (pathogenic for Brachydactyly type A2|Fibular hypoplasia and complex brachydactyly) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM021270)

known disease mutation at this position, please check HGMD for details (HGMD ID CM021270)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021270)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0850.994
4.6711
(flanking)1.0691
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 increased20670wt: 0.4269 / mu: 0.4621 (marginal change - not scored)wt: CTGTGCGAGTTCCCATTGCGCTCCCACCTGGAGCCCACGAA
mu: CTGTGCGAGTTCCCATTGCGCTCCCACCCGGAGCCCACGAA		 gcgc|TCCC
Acc increased20675wt: 0.50 / mu: 0.65wt: CGAGTTCCCATTGCGCTCCCACCTGGAGCCCACGAATCATG
mu: CGAGTTCCCATTGCGCTCCCACCCGGAGCCCACGAATCATG		 ccca|CCTG
Acc marginally increased20680wt: 0.6541 / mu: 0.6584 (marginal change - not scored)wt: TCCCATTGCGCTCCCACCTGGAGCCCACGAATCATGCAGTC
mu: TCCCATTGCGCTCCCACCCGGAGCCCACGAATCATGCAGTC		 ctgg|AGCC
Acc marginally increased20679wt: 0.6654 / mu: 0.7198 (marginal change - not scored)wt: TTCCCATTGCGCTCCCACCTGGAGCCCACGAATCATGCAGT
mu: TTCCCATTGCGCTCCCACCCGGAGCCCACGAATCATGCAGT		 cctg|GAGC
distance from splice site 691
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      441EGLCEFPLRSHLEPTNHAVIQTLM
mutated  not conserved    441EGLCEFPLRSHPEPTNHAVIQTL
Ptroglodytes  all identical  ENSPTRG00000013439  441EGLCEFPLRSHLEPTNHAVIQTL
Mmulatta  all identical  ENSMMUG00000007333  439EGLCEFPLRSHLEPTNHAVIQTL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038259  435EGLCEFPLRSHLEPTNHAVIQTL
Ggallus  all identical  ENSGALG00000001786  440EGLCEFPLRSHLEPTNHAVIQTL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000002760  414DGVCDFPIRSHLEPTNHAIIQTL
Dmelanogaster  not conserved  FBgn0000490  528HGKCPFPLADHFNSTNHAVVQTL
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021223  436EGLCEFPLRSHLEPTNHAVIQTL
protein features
start (aa)end (aa)featuredetails 
439441HELIXlost
445456HELIXmight get lost (downstream of altered splice site)
458460TURNmight get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
465465DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
466466DISULFIDmight get lost (downstream of altered splice site)
466479STRANDmight get lost (downstream of altered splice site)
481483STRANDmight get lost (downstream of altered splice site)
485500STRANDmight get lost (downstream of altered splice site)
498498DISULFIDmight get lost (downstream of altered splice site)
500500DISULFIDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1506 / 1506
position (AA) of stopcodon in wt / mu AA sequence 502 / 502
position of stopcodon in wt / mu cDNA 1821 / 1821
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 316 / 316
chromosome 20
strand -1
last intron/exon boundary 947
theoretical NMD boundary in CDS 581
length of CDS 1506
coding sequence (CDS) position 1322
cDNA position
(for ins/del: last normal base / first normal base)		 1637
gDNA position
(for ins/del: last normal base / first normal base)		 20678
chromosomal position
(for ins/del: last normal base / first normal base)		 34021891
original gDNA sequence snippet GTTCCCATTGCGCTCCCACCTGGAGCCCACGAATCATGCAG
altered gDNA sequence snippet GTTCCCATTGCGCTCCCACCCGGAGCCCACGAATCATGCAG
original cDNA sequence snippet GTTCCCATTGCGCTCCCACCTGGAGCCCACGAATCATGCAG
altered cDNA sequence snippet GTTCCCATTGCGCTCCCACCCGGAGCCCACGAATCATGCAG
wildtype AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
mutated AA sequence MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH PEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*
speed 0.99 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