Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000264167
Querying Taster for transcript #2: ENST00000409888
MT speed 2.7 s - this script 8.744515 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGPSdisease_causing_automatic0.999999769739283simple_aaeaffected0T309Isingle base exchangers121434412show file
AGPSdisease_causing_automatic1without_aaeaffected0single base exchangers121434412show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999769739283 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012330)
  • known disease mutation: rs6646 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:178326676C>TN/A show variant in all transcripts   IGV
HGNC symbol AGPS
Ensembl transcript ID ENST00000264167
Genbank transcript ID NM_003659
UniProt peptide O00116
alteration type single base exchange
alteration region CDS
DNA changes c.926C>T
cDNA.1072C>T
g.69305C>T
AA changes T309I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
309
frameshift no
known variant Reference ID: rs121434412
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs6646 (pathogenic for Rhizomelic chondrodysplasia punctata type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0351
5.7921
(flanking)0.0290.986
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69301wt: 0.60 / mu: 0.93wt: AGTTCAGTACTGTAG
mu: AGTTCAGTATTGTAG
 TTCA|gtac
Acc gained693100.31mu: CCCTGGAGTTCAGTATTGTAGGAGGATGGGTATCTACTCGC gtag|GAGG
distance from splice site 56
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      309TGHEPDSLEFSTVGGWVSTRASGM
mutated  not conserved    309EPDSLEFSIVGGWVSTRASG
Ptroglodytes  all identical  ENSPTRG00000012680  309EPDSLEFSTVGGWVSTRASG
Mmulatta  all identical  ENSMMUG00000008502  310TGHEPDSLEFSTVGGWVSTRASG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000042410  322TGHEPDSLEFSTVGGWI
Ggallus  all conserved  ENSGALG00000009236  289TGHEPDSMEFSSLGGWVATRASG
Trubripes  all conserved  ENSTRUG00000017479  295TGHEPDSMEFSSLG
Drerio  all conserved  ENSDARG00000042821  280TGHEPDSMEFSSLGGWVATRASG
Dmelanogaster  all identical  FBgn0033983  262VGHEPDSYEFSTLGGWVATRASG
Celegans  all identical  Y50D7A.7  238CGHEPDSIEFSTLGGWVSTRASG
Xtropicalis  all identical  ENSXETG00000008462  278TGHEPDSMEFSTLGGWVATRASG
protein features
start (aa)end (aa)featuredetails 
202384DOMAINFAD-binding PCMH-type.lost
347347MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
578578ACT_SITEBy 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 2123 / 2123
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 147 / 147
chromosome 2
strand 1
last intron/exon boundary 2002
theoretical NMD boundary in CDS 1805
length of CDS 1977
coding sequence (CDS) position 926
cDNA position
(for ins/del: last normal base / first normal base)
1072
gDNA position
(for ins/del: last normal base / first normal base)
69305
chromosomal position
(for ins/del: last normal base / first normal base)
178326676
original gDNA sequence snippet AGATTCCCTGGAGTTCAGTACTGTAGGAGGATGGGTATCTA
altered gDNA sequence snippet AGATTCCCTGGAGTTCAGTATTGTAGGAGGATGGGTATCTA
original cDNA sequence snippet AGATTCCCTGGAGTTCAGTACTGTAGGAGGATGGGTATCTA
altered cDNA sequence snippet AGATTCCCTGGAGTTCAGTATTGTAGGAGGATGGGTATCTA
wildtype AA sequence MAEAAAAAGG TGLGAGASYG SAADRDRDPD PDRAGRRLRV LSGHLLGRPR EALSTNECKA
RRAASAATAA PTATPAAQES GTIPKKRQEV MKWNGWGYND SKFIFNKKGQ IELTGKRYPL
SGMGLPTFKE WIQNTLGVNV EHKTTSKASL NPSDTPPSVV NEDFLHDLKE TNISYSQEAD
DRVFRAHGHC LHEIFLLREG MFERIPDIVL WPTCHDDVVK IVNLACKYNL CIIPIGGGTS
VSYGLMCPAD ETRTIISLDT SQMNRILWVD ENNLTAHVEA GITGQELERQ LKESGYCTGH
EPDSLEFSTV GGWVSTRASG MKKNIYGNIE DLVVHIKMVT PRGIIEKSCQ GPRMSTGPDI
HHFIMGSEGT LGVITEATIK IRPVPEYQKY GSVAFPNFEQ GVACLREIAK QRCAPASIRL
MDNKQFQFGH ALKPQVSSIF TSFLDGLKKF YITKFKGFDP NQLSVATLLF EGDREKVLQH
EKQVYDIAAK FGGLAAGEDN GQRGYLLTYV IAYIRDLALE YYVLGESFET SAPWDRVVDL
CRNVKERITR ECKEKGVQFA PFSTCRVTQT YDAGACIYFY FAFNYRGISD PLTVFEQTEA
AAREEILANG GSLSHHHGVG KLRKQWLKES ISDVGFGMLK SVKEYVDPNN IFGNRNLL*
mutated AA sequence MAEAAAAAGG TGLGAGASYG SAADRDRDPD PDRAGRRLRV LSGHLLGRPR EALSTNECKA
RRAASAATAA PTATPAAQES GTIPKKRQEV MKWNGWGYND SKFIFNKKGQ IELTGKRYPL
SGMGLPTFKE WIQNTLGVNV EHKTTSKASL NPSDTPPSVV NEDFLHDLKE TNISYSQEAD
DRVFRAHGHC LHEIFLLREG MFERIPDIVL WPTCHDDVVK IVNLACKYNL CIIPIGGGTS
VSYGLMCPAD ETRTIISLDT SQMNRILWVD ENNLTAHVEA GITGQELERQ LKESGYCTGH
EPDSLEFSIV GGWVSTRASG MKKNIYGNIE DLVVHIKMVT PRGIIEKSCQ GPRMSTGPDI
HHFIMGSEGT LGVITEATIK IRPVPEYQKY GSVAFPNFEQ GVACLREIAK QRCAPASIRL
MDNKQFQFGH ALKPQVSSIF TSFLDGLKKF YITKFKGFDP NQLSVATLLF EGDREKVLQH
EKQVYDIAAK FGGLAAGEDN GQRGYLLTYV IAYIRDLALE YYVLGESFET SAPWDRVVDL
CRNVKERITR ECKEKGVQFA PFSTCRVTQT YDAGACIYFY FAFNYRGISD PLTVFEQTEA
AAREEILANG GSLSHHHGVG KLRKQWLKES ISDVGFGMLK SVKEYVDPNN IFGNRNLL*
speed 1.50 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
back to results table
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 CM012330)
  • known disease mutation: rs6646 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:178326676C>TN/A show variant in all transcripts   IGV
HGNC symbol AGPS
Ensembl transcript ID ENST00000409888
Genbank transcript ID N/A
UniProt peptide O00116
alteration type single base exchange
alteration region intron
DNA changes g.69305C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121434412
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs6646 (pathogenic for Rhizomelic chondrodysplasia punctata type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012330)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0351
5.7921
(flanking)0.0290.986
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69301wt: 0.60 / mu: 0.93wt: AGTTCAGTACTGTAG
mu: AGTTCAGTATTGTAG
 TTCA|gtac
Acc gained693100.31mu: CCCTGGAGTTCAGTATTGTAGGAGGATGGGTATCTACTCGC gtag|GAGG
distance from splice site 41590
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
169169MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
202384DOMAINFAD-binding PCMH-type.might get lost (downstream of altered splice site)
347347MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
578578ACT_SITEBy similarity.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 23 / 23
chromosome 2
strand 1
last intron/exon boundary 471
theoretical NMD boundary in CDS 398
length of CDS 570
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)
69305
chromosomal position
(for ins/del: last normal base / first normal base)
178326676
original gDNA sequence snippet AGATTCCCTGGAGTTCAGTACTGTAGGAGGATGGGTATCTA
altered gDNA sequence snippet AGATTCCCTGGAGTTCAGTATTGTAGGAGGATGGGTATCTA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAEAAAAAGG TGLGAGASYG SAADRDRDPD PDRAGRRLRV LSGHLLGRPR EALSTNECKA
RRAASAATAA PTATPAAQES GTIPKKRQEV MKWNGWGYND SKFIFNKKGQ IELTGKRGIS
DPLTVFEQTE AAAREEILAN GGSLSHHHGV GKLRKQWLKE SISDVGFGML KSVKEYVDPN
NIFGNRNLL*
mutated AA sequence N/A
speed 1.20 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
back to results table

Problems