MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000264093
Querying Taster for transcript #2: ENST00000348222
Querying Taster for transcript #3: ENST00000356837
MT speed 0 s - this script 3.109151 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DGUOK	disease_causing_automatic	0.999999999501644	simple_aae		affected	0	E227K	single base exchange	rs104893632		show file
DGUOK	disease_causing_automatic	0.999999999501644	simple_aae		affected	0	E205K	single base exchange	rs104893632		show file
DGUOK	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs104893632		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999501644 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024769)
known disease mutation: rs8158 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:74184339G>AN/A show variant in all transcripts IGV

HGNC symbol

DGUOK

Ensembl transcript ID

ENST00000264093

Genbank transcript ID

NM_080916

UniProt peptide

Q16854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.679G>A
cDNA.764G>A
g.30387G>A

AA changes

E227K Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

227

frameshift

known variant

Reference ID: rs104893632
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8158 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024769)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024769)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024769)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.123	0.99
	4.508	1
(flanking)	3.734	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	30384	wt: 0.9314 / mu: 0.9547 (marginal change - not scored)	wt: GCCAACACGAAGCCT mu: GCCAACACAAAGCCT	CAAC\|acga
Donor increased	30389	wt: 0.76 / mu: 0.86	wt: CACGAAGCCTGGCTT mu: CACAAAGCCTGGCTT	CGAA\|gcct
Donor gained	30383	0.92	mu: GGCCAACACAAAGCC	CCAA\|caca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

227

mutated

all conserved

227

Ptroglodytes

all identical

ENSPTRG00000012074

227

Mmulatta

all identical

ENSMMUG00000017830

227

Fcatus

all identical

ENSFCAG00000012099

227

Mmusculus

all identical

ENSMUSG00000014554

227

Ggallus

all identical

ENSGALG00000022134

Trubripes

all identical

ENSTRUG00000012499

216

Drerio

all identical

ENSDARG00000075395

219

Dmelanogaster

all identical

FBgn0022338

188

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019642

211

protein features

start (aa)	end (aa)	feature	details
216	230	HELIX		lost
242	244	HELIX		might get lost (downstream of altered splice site)
247	251	STRAND		might get lost (downstream of altered splice site)
256	258	TURN		might get lost (downstream of altered splice site)
260	275	HELIX		might get lost (downstream of altered splice site)
275	275	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

834 / 834

position (AA) of stopcodon in wt / mu AA sequence

278 / 278

position of stopcodon in wt / mu cDNA

919 / 919

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

86 / 86

chromosome

strand

last intron/exon boundary

893

theoretical NMD boundary in CDS

757

length of CDS

834

coding sequence (CDS) position

679

cDNA position
(for ins/del: last normal base / first normal base)

764

gDNA position
(for ins/del: last normal base / first normal base)

30387

chromosomal position
(for ins/del: last normal base / first normal base)

74184339

original gDNA sequence snippet

AGCAGCTGCATGGCCAACACGAAGCCTGGCTTATTCACAAG

altered gDNA sequence snippet

AGCAGCTGCATGGCCAACACAAAGCCTGGCTTATTCACAAG

original cDNA sequence snippet

AGCAGCTGCATGGCCAACACGAAGCCTGGCTTATTCACAAG

altered cDNA sequence snippet

AGCAGCTGCATGGCCAACACAAAGCCTGGCTTATTCACAAG

wildtype AA sequence

MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF ERSVYSDRYI FAKNLFENGS LSDIEWHIYQ DWHSFLLWEF
ASRITLHGFI YLQASPQVCL KRLYQRAREE EKGIELAYLE QLHGQHEAWL IHKTTKLHFE
ALMNIPVLVL DVNDDFSEEV TKQEDLMREV NTFVKNL*

mutated AA sequence

MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF ERSVYSDRYI FAKNLFENGS LSDIEWHIYQ DWHSFLLWEF
ASRITLHGFI YLQASPQVCL KRLYQRAREE EKGIELAYLE QLHGQHKAWL IHKTTKLHFE
ALMNIPVLVL DVNDDFSEEV TKQEDLMREV NTFVKNL*

speed

0.42 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999501644 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024769)
known disease mutation: rs8158 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:74184339G>AN/A show variant in all transcripts IGV

HGNC symbol

DGUOK

Ensembl transcript ID

ENST00000356837

Genbank transcript ID

N/A

UniProt peptide

Q16854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.613G>A
cDNA.616G>A
g.30387G>A

AA changes

E205K Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

205

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.123	0.99
	4.508	1
(flanking)	3.734	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	30384	wt: 0.9314 / mu: 0.9547 (marginal change - not scored)	wt: GCCAACACGAAGCCT mu: GCCAACACAAAGCCT	CAAC\|acga
Donor increased	30389	wt: 0.76 / mu: 0.86	wt: CACGAAGCCTGGCTT mu: CACAAAGCCTGGCTT	CGAA\|gcct
Donor gained	30383	0.92	mu: GGCCAACACAAAGCC	CCAA\|caca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

205

mutated

all conserved

205

Ptroglodytes

all identical

ENSPTRG00000012074

227

Mmulatta

all identical

ENSMMUG00000017830

227

Fcatus

all identical

ENSFCAG00000012099

227

Mmusculus

all identical

ENSMUSG00000014554

227

Ggallus

all identical

ENSGALG00000022134

Trubripes

all identical

ENSTRUG00000012499

216

Drerio

all identical

ENSDARG00000075395

219

Dmelanogaster

all identical

FBgn0022338

188

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019642

211

protein features

start (aa)	end (aa)	feature	details
196	205	HELIX		lost
206	208	NP_BIND	ATP.	might get lost (downstream of altered splice site)
209	213	TURN		might get lost (downstream of altered splice site)
211	211	BINDING	Substrate.	might get lost (downstream of altered splice site)
212	212	CONFLICT	K -> E (in Ref. 5; CAA66054).	might get lost (downstream of altered splice site)
216	230	HELIX		might get lost (downstream of altered splice site)
242	244	HELIX		might get lost (downstream of altered splice site)
247	251	STRAND		might get lost (downstream of altered splice site)
256	258	TURN		might get lost (downstream of altered splice site)
260	275	HELIX		might get lost (downstream of altered splice site)
275	275	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

768 / 768

position (AA) of stopcodon in wt / mu AA sequence

256 / 256

position of stopcodon in wt / mu cDNA

771 / 771

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

4 / 4

chromosome

strand

last intron/exon boundary

745

theoretical NMD boundary in CDS

691

length of CDS

768

coding sequence (CDS) position

613

cDNA position
(for ins/del: last normal base / first normal base)

616

gDNA position
(for ins/del: last normal base / first normal base)

30387

chromosomal position
(for ins/del: last normal base / first normal base)

74184339

original gDNA sequence snippet

AGCAGCTGCATGGCCAACACGAAGCCTGGCTTATTCACAAG

altered gDNA sequence snippet

AGCAGCTGCATGGCCAACACAAAGCCTGGCTTATTCACAAG

original cDNA sequence snippet

AGCAGCTGCATGGCCAACACGAAGCCTGGCTTATTCACAAG

altered cDNA sequence snippet

AGCAGCTGCATGGCCAACACAAAGCCTGGCTTATTCACAAG

wildtype AA sequence

MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIGNI LKQIRMRAPI
QETACTAQSL GNLLDMMYRE PARWSYTFQT FSFLSRLKVQ LEPFPEKLLQ ARKPVQIFER
SVYSDRYIFA KNLFENGSLS DIEWHIYQDW HSFLLWEFAS RITLHGFIYL QASPQVCLKR
LYQRAREEEK GIELAYLEQL HGQHEAWLIH KTTKLHFEAL MNIPVLVLDV NDDFSEEVTK
QEDLMREVNT FVKNL*

mutated AA sequence

MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIGNI LKQIRMRAPI
QETACTAQSL GNLLDMMYRE PARWSYTFQT FSFLSRLKVQ LEPFPEKLLQ ARKPVQIFER
SVYSDRYIFA KNLFENGSLS DIEWHIYQDW HSFLLWEFAS RITLHGFIYL QASPQVCLKR
LYQRAREEEK GIELAYLEQL HGQHKAWLIH KTTKLHFEAL MNIPVLVLDV NDDFSEEVTK
QEDLMREVNT FVKNL*

speed

0.76 s

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 CM024769)
known disease mutation: rs8158 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:74184339G>AN/A show variant in all transcripts IGV

HGNC symbol

DGUOK

Ensembl transcript ID

ENST00000348222

Genbank transcript ID

NM_080918

UniProt peptide

Q16854

alteration type

single base exchange

alteration region

intron

DNA changes

g.30387G>A

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.123	0.99
	4.508	1
(flanking)	3.734	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	30384	wt: 0.9314 / mu: 0.9547 (marginal change - not scored)	wt: GCCAACACGAAGCCT mu: GCCAACACAAAGCCT	CAAC\|acga
Donor increased	30389	wt: 0.76 / mu: 0.86	wt: CACGAAGCCTGGCTT mu: CACAAAGCCTGGCTT	CGAA\|gcct
Donor gained	30383	0.92	mu: GGCCAACACAAAGCC	CCAA\|caca

distance from splice site

934

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
144	149	HELIX		might get lost (downstream of altered splice site)
151	157	HELIX		might get lost (downstream of altered splice site)
159	159	CONFLICT	G -> D (in Ref. 5; CAA66054).	might get lost (downstream of altered splice site)
163	179	HELIX		might get lost (downstream of altered splice site)
181	184	HELIX		might get lost (downstream of altered splice site)
188	193	STRAND		might get lost (downstream of altered splice site)
196	205	HELIX		might get lost (downstream of altered splice site)
206	208	NP_BIND	ATP.	might get lost (downstream of altered splice site)
209	213	TURN		might get lost (downstream of altered splice site)
211	211	BINDING	Substrate.	might get lost (downstream of altered splice site)
212	212	CONFLICT	K -> E (in Ref. 5; CAA66054).	might get lost (downstream of altered splice site)
216	230	HELIX		might get lost (downstream of altered splice site)
242	244	HELIX		might get lost (downstream of altered splice site)
247	251	STRAND		might get lost (downstream of altered splice site)
256	258	TURN		might get lost (downstream of altered splice site)
260	275	HELIX		might get lost (downstream of altered splice site)
275	275	MOD_RES	N6-acetyllysine.	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

86 / 86

chromosome

strand

last intron/exon boundary

629

theoretical NMD boundary in CDS

493

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)

30387

chromosomal position
(for ins/del: last normal base / first normal base)

74184339

original gDNA sequence snippet

AGCAGCTGCATGGCCAACACGAAGCCTGGCTTATTCACAAG

altered gDNA sequence snippet

AGCAGCTGCATGGCCAACACAAAGCCTGGCTTATTCACAAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF ERSVYSDRLH FEALMNIPVL VLDVNDDFSE EVTKQEDLMR
EVNTFVKNL*

mutated AA sequence

N/A

speed

0.35 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems