Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998366161 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950320)
  • known disease mutation: rs9187 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:18898411C>AN/A show variant in all transcripts   IGV
HGNC symbol COMP
Ensembl transcript ID ENST00000542601
Genbank transcript ID N/A
UniProt peptide P49747
alteration type single base exchange
alteration region CDS
DNA changes c.925G>T
cDNA.1315G>T
g.3713G>T
AA changes D309Y Score: 160 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 309
frameshift no
known variant Reference ID: rs137852652
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs9187 (pathogenic for Epiphyseal dysplasia, multiple, 1, severe) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950320)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950320)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950320)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9711
4.8090.998
(flanking)-0.1850.079
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 increased3717wt: 0.9543 / mu: 0.9794 (marginal change - not scored)wt: GGACAAGTGGGGCGA
mu: GTACAAGTGGGGCGA		 ACAA|gtgg
Donor marginally increased3704wt: 0.6910 / mu: 0.7579 (marginal change - not scored)wt: GCAACACGGACGAGG
mu: GCAACACGGACGAGT		 AACA|cgga
distance from splice site 49
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      309VRNPDQRNTDEDKWGDACDNCRSQ
mutated  not conserved    309PDQRNTDEYKWGDACDNCRS
Ptroglodytes  all identical  ENSPTRG00000010720  322VRNPDQRNTDEDKWGDACDNCRS
Mmulatta  all identical  ENSMMUG00000006511  342PDQRNTDEDKWGDACDNCRT
Fcatus  all identical  ENSFCAG00000009754  343VRNPDQRNADGDKWGDACDNCRS
Mmusculus  all identical  ENSMUSG00000031849  340PDQRNSDSDKWGDACDNCRS
Ggallus  all identical  ENSGALG00000003283  342NADQRNADKDNFGDACDNCRL
Trubripes  all identical  ENSTRUG00000007160  310PNMDQRNVDEDDFGDACDNCPG
Drerio  all identical  ENSDARG00000053865  327VNQKNTDQDDYGDACDNCRL
Dmelanogaster  all identical  FBgn0031850  637DSDGDKVGDVCDNCVL
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000011202  337RPSQKTLVLKENRKLKSPWGGGGGNLLG
protein features
start (aa)end (aa)featuredetails 
301336REPEATTSP type-3 2.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2175 / 2175
position (AA) of stopcodon in wt / mu AA sequence 725 / 725
position of stopcodon in wt / mu cDNA 2565 / 2565
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 391 / 391
chromosome 19
strand -1
last intron/exon boundary 2519
theoretical NMD boundary in CDS 2078
length of CDS 2175
coding sequence (CDS) position 925
cDNA position
(for ins/del: last normal base / first normal base)		 1315
gDNA position
(for ins/del: last normal base / first normal base)		 3713
chromosomal position
(for ins/del: last normal base / first normal base)		 18898411
original gDNA sequence snippet ACCAGCGCAACACGGACGAGGACAAGTGGGGCGATGCGTGC
altered gDNA sequence snippet ACCAGCGCAACACGGACGAGTACAAGTGGGGCGATGCGTGC
original cDNA sequence snippet ACCAGCGCAACACGGACGAGGACAAGTGGGGCGATGCGTGC
altered cDNA sequence snippet ACCAGCGCAACACGGACGAGTACAAGTGGGGCGATGCGTGC
wildtype AA sequence MLRELQETNA ALQDVRELLR QQVREITFLK NTVMECDACG MQQSVRTGLP SVRPLLHCAP
GFCFPGVACI QTESGARCGP CPAGFTGNGS HCTDVNECNA HPCFPRVRCI NTSPGFRCEA
CPPGYSGPTH QGVGLAFAKA NKQVCTDINE CETGQHNCVP NSVCINTRGS FQCGPCQPGF
VGDQASGCQR RAQRFCPDGS PSECHEHADC VLERDGSRSC VCAVGWAGNG ILCGRDTDLD
GFPDEKLRCP ERQCRKDNCV TVPNSGQEDV DRDGIGDACD PDADGDGVPN EKDNCPLVRN
PDQRNTDEDK WGDACDNCRS QKNDDQKDTD QDGRGDACDD DIDGDRIRNQ ADNCPRVPNS
DQKDSDGDGI GDACDNCPQK SNPDQADVDH DFVGDACDSD QDQDGDGHQD SRDNCPTVPN
SAQEDSDHDG QGDACDDDDD NDGVPDSRDN CRLVPNPGQE DADRDGVGDV CQDDFDADKV
VDKIDVCPEN AEVTLTDFRA FQTVVLDPEG DAQIDPNWVV LNQGREIVQT MNSDPGLAVG
YTAFNGVDFE GTFHVNTVTD DDYAGFIFGY QDSSSFYVVM WKQMEQTYWQ ANPFRAVAEP
GIQLKAVKSS TGPGEQLRNA LWHTGDTESQ VRLLWKDPRN VGWKDKKSYR WFLQHRPQVG
YIRVRFYEGP ELVADSNVVL DTTMRGGRLG VFCFSQENII WANLRYRCND TIPEDYETHQ
LRQA*
mutated AA sequence MLRELQETNA ALQDVRELLR QQVREITFLK NTVMECDACG MQQSVRTGLP SVRPLLHCAP
GFCFPGVACI QTESGARCGP CPAGFTGNGS HCTDVNECNA HPCFPRVRCI NTSPGFRCEA
CPPGYSGPTH QGVGLAFAKA NKQVCTDINE CETGQHNCVP NSVCINTRGS FQCGPCQPGF
VGDQASGCQR RAQRFCPDGS PSECHEHADC VLERDGSRSC VCAVGWAGNG ILCGRDTDLD
GFPDEKLRCP ERQCRKDNCV TVPNSGQEDV DRDGIGDACD PDADGDGVPN EKDNCPLVRN
PDQRNTDEYK WGDACDNCRS QKNDDQKDTD QDGRGDACDD DIDGDRIRNQ ADNCPRVPNS
DQKDSDGDGI GDACDNCPQK SNPDQADVDH DFVGDACDSD QDQDGDGHQD SRDNCPTVPN
SAQEDSDHDG QGDACDDDDD NDGVPDSRDN CRLVPNPGQE DADRDGVGDV CQDDFDADKV
VDKIDVCPEN AEVTLTDFRA FQTVVLDPEG DAQIDPNWVV LNQGREIVQT MNSDPGLAVG
YTAFNGVDFE GTFHVNTVTD DDYAGFIFGY QDSSSFYVVM WKQMEQTYWQ ANPFRAVAEP
GIQLKAVKSS TGPGEQLRNA LWHTGDTESQ VRLLWKDPRN VGWKDKKSYR WFLQHRPQVG
YIRVRFYEGP ELVADSNVVL DTTMRGGRLG VFCFSQENII WANLRYRCND TIPEDYETHQ
LRQA*
speed 1.13 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