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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000367435
MT speed 0 s - this script 2.872004 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CDC73disease_causing_automatic1simple_aaeaffected0L64Psingle base exchangers121434264show file

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Prediction

disease causing

 Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032272)
  • known disease mutation: rs3272 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:193094301T>CN/A show variant in all transcripts   IGV
HGNC symbol CDC73
Ensembl transcript ID ENST00000367435
Genbank transcript ID NM_024529
UniProt peptide Q6P1J9
alteration type single base exchange
alteration region CDS
DNA changes c.191T>C
cDNA.375T>C
g.3155T>C
AA changes L64P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 64
frameshift no
known variant Reference ID: rs121434264
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3272 (pathogenic for Hyperparathyroidism 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032272)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032272)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032272)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.31
4.9191
(flanking)0.0510.995
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 increased3152wt: 0.5782 / mu: 0.6307 (marginal change - not scored)wt: ATTGGATTCCATTTTATTTCTACTTAATAACGTGCACCTTT
mu: ATTGGATTCCATTTTATTTCTACCTAATAACGTGCACCTTT		 ttct|ACTT
Acc marginally increased3156wt: 0.9761 / mu: 0.9765 (marginal change - not scored)wt: GATTCCATTTTATTTCTACTTAATAACGTGCACCTTTCTCA
mu: GATTCCATTTTATTTCTACCTAATAACGTGCACCTTTCTCA		 actt|AATA
Acc increased3148wt: 0.28 / mu: 0.37wt: ACACATTGGATTCCATTTTATTTCTACTTAATAACGTGCAC
mu: ACACATTGGATTCCATTTTATTTCTACCTAATAACGTGCAC		 ttat|TTCT
Acc marginally increased3150wt: 0.8608 / mu: 0.8826 (marginal change - not scored)wt: ACATTGGATTCCATTTTATTTCTACTTAATAACGTGCACCT
mu: ACATTGGATTCCATTTTATTTCTACCTAATAACGTGCACCT		 attt|CTAC
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      64EYYTLDSILFLLNNVHLSHPVYVR
mutated  not conserved    64LFLPNNVHLSHPVYV
Ptroglodytes  all identical  ENSPTRG00000001796  64LFLLNNVHLSHPVYV
Mmulatta  all identical  ENSMMUG00000022647  64LFLLNNVHLSHPVYV
Fcatus  all identical  ENSFCAG00000000348  64LFLLNNVHLSHPVYV
Mmusculus  all identical  ENSMUSG00000026361  64LFLLNNVHLSHPVYV
Ggallus  all identical  ENSGALG00000002469  64LFLLNNVHLSHPVYV
Trubripes  all identical  ENSTRUG00000009352  64LFLLNNVHLPHPSYV
Drerio  all identical  ENSDARG00000020201  64LFLLNNVHLPHPSYV
Dmelanogaster  all identical  FBgn0037657  64LYLLKNVMLQHSVYV
Celegans  all identical  F35F11.1  68-FYSLESLVVFLK
Xtropicalis  all identical  ENSXETG00000004533  64LFLLNNVHLSHPVYV
protein features
start (aa)end (aa)featuredetails 
123123CONFLICTQ -> G (in Ref. 5; AAH14351).might get lost (downstream of altered splice site)
125139MOTIFNuclear localization signal.might get lost (downstream of altered splice site)
174174MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
178178MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
184187CONFLICTAIKA -> CNQT (in Ref. 2; BAB15608).might get lost (downstream of altered splice site)
200250REGIONInteraction with CTNNB1.might get lost (downstream of altered splice site)
200531REGIONInteraction with POLR2A and PAF1.might get lost (downstream of altered splice site)
212212MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
361364COMPBIASPoly-Ile.might get lost (downstream of altered splice site)
372372CONFLICTI -> K (in Ref. 2; BAB15608).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1596 / 1596
position (AA) of stopcodon in wt / mu AA sequence 532 / 532
position of stopcodon in wt / mu cDNA 1780 / 1780
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 185 / 185
chromosome 1
strand 1
last intron/exon boundary 1744
theoretical NMD boundary in CDS 1509
length of CDS 1596
coding sequence (CDS) position 191
cDNA position
(for ins/del: last normal base / first normal base)		 375
gDNA position
(for ins/del: last normal base / first normal base)		 3155
chromosomal position
(for ins/del: last normal base / first normal base)		 193094301
original gDNA sequence snippet GGATTCCATTTTATTTCTACTTAATAACGTGCACCTTTCTC
altered gDNA sequence snippet GGATTCCATTTTATTTCTACCTAATAACGTGCACCTTTCTC
original cDNA sequence snippet GGATTCCATTTTATTTCTACTTAATAACGTGCACCTTTCTC
altered cDNA sequence snippet GGATTCCATTTTATTTCTACCTAATAACGTGCACCTTTCTC
wildtype AA sequence MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLLNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRTRTTILQS
TGKNFSKNIF AILQSVKARE EGRAPEQRPA PNAAPVDPTL RTKQPIPAAY NRYDQERFKG
KEETEGFKID TMGTYHGMTL KSVTEGASAR KTQTPAAQPV PRPVSQARPP PNQKKGSRTP
IIIIPAATTS LITMLNAKDL LQDLKFVPSD EKKKQGCQRE NETLIQRRKD QMQPGGTAIS
VTVPYRVVDQ PLKLMPQDWD RVVAVFVQGP AWQFKGWPWL LPDGSPVDIF AKIKAFHLKY
DEVRLDPNVQ KWDVTVLELS YHKRHLDRPV FLRFWETLDR YMVKHKSHLR F*
mutated AA sequence MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI
LFLPNNVHLS HPVYVRRAAT ENIPVVRRPD RKDLLGYLNG EASTSASIDR SAPLEIGLQR
STQVKRAADE VLAEAKKPRI EDEECVRLDK ERLAARLEGH KEGIVQTEQI RSLSEAMSVE
KIAAIKAKIM AKKRSTIKTD LDDDITALKQ RSFVDAEVDV TRDIVSRERV WRTRTTILQS
TGKNFSKNIF AILQSVKARE EGRAPEQRPA PNAAPVDPTL RTKQPIPAAY NRYDQERFKG
KEETEGFKID TMGTYHGMTL KSVTEGASAR KTQTPAAQPV PRPVSQARPP PNQKKGSRTP
IIIIPAATTS LITMLNAKDL LQDLKFVPSD EKKKQGCQRE NETLIQRRKD QMQPGGTAIS
VTVPYRVVDQ PLKLMPQDWD RVVAVFVQGP AWQFKGWPWL LPDGSPVDIF AKIKAFHLKY
DEVRLDPNVQ KWDVTVLELS YHKRHLDRPV FLRFWETLDR YMVKHKSHLR F*
speed 0.80 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
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Problems