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: ENST00000252711
Querying Taster for transcript #2: ENST00000404554
Querying Taster for transcript #3: ENST00000307300
MT speed 0 s - this script 3.112077 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NDUFA10	polymorphism_automatic	5.99520433297585e-15	simple_aae				V392M	single base exchange	rs1530144		show file
NDUFA10	polymorphism_automatic	7.74062830499744e-08	without_aae					single base exchange	rs1530144		show file
NDUFA10	polymorphism_automatic	7.74062830499744e-08	without_aae					single base exchange	rs1530144		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999994 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:240923050C>TN/A show variant in all transcripts IGV

HGNC symbol

NDUFA10

Ensembl transcript ID

ENST00000307300

Genbank transcript ID

N/A

UniProt peptide

O95299

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1174G>A
cDNA.1197G>A
g.41770G>A

AA changes

V392M Score: 21 explain score(s)

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

392

frameshift

known variant

Reference ID: rs1530144

database	homozygous (T/T)	heterozygous	allele carriers
1000G	439	1197	1636
ExAC	5241	16101	21342

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.004	0.004
	-0.341	0.003
(flanking)	-2.099	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

392

mutated

all conserved

392

Ptroglodytes

no alignment

ENSPTRG00000013099

n/a

Mmulatta

all conserved

ENSMMUG00000010382

392

Fcatus

no alignment

ENSFCAG00000002205

n/a

Mmusculus

no alignment

ENSMUSG00000026260

n/a

Ggallus

no alignment

ENSGALG00000004302

n/a

Trubripes

no alignment

ENSTRUG00000009422

n/a

Drerio

no alignment

ENSDARG00000013333

n/a

Dmelanogaster

no alignment

FBgn0019957

n/a

Celegans

no alignment

K04G7.4

n/a

Xtropicalis

no alignment

ENSXETG00000004886

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1290 / 1290

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

430 / 430

position of stopcodon in wt / mu cDNA

1313 / 1313

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

24 / 24

chromosome

strand

-1

last intron/exon boundary

1113

theoretical NMD boundary in CDS

1039

length of CDS

1290

coding sequence (CDS) position

1174

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

1197

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

41770

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

240923050

original gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCGTGGCCCTGACCGTGGGCTCC

altered gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCATGGCCCTGACCGTGGGCTCC

original cDNA sequence snippet

TGTCAGTGCAGCCTGGCACCGTGGCCCTGACCGTGGGCTCC

altered cDNA sequence snippet

TGTCAGTGCAGCCTGGCACCATGGCCCTGACCGTGGGCTCC

wildtype AA sequence

MALRLLKLAA TSASARVVAA GAQRVRGIHS SVQCKLRYGM WHFLLGDKAS KRLTERSRVI
TVDGNICTGK GKLAKEIAEK LGFKHFPEAG IHYPDSTTGD GKPLATDYNG NCSLEKFYDD
PRSNDGNSYR LQSWLYSSRL LQYSDALEHL LTTGQGVVLE RSIFSDFVFL EAMYNQGFIR
KQCESALQTH FWTGVAGASG KLESGSSEEV LLINERGGRS KPGVDHYNEV KSVTICDYLP
PHLVIYIDVP VPEPHEMKIT SAYLQDIENA YKKTFLPEMS EKCEVLQYSA REAQDSKKVV
EDIEYLKFDK GPWLKQDNRT LYHLRLLVQD KFEVLNYTSI PIFLPEVTIG AHQTDRVLHQ
FRERLDWTVC FGEESTEVKH QGHLLSVQPG TVALTVGSWL RSCLLGLHWK LLFLFPESPM
HTTAFMFLC*

mutated AA sequence

speed

0.43 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

polymorphism

Model: without_aae, prob: 0.999999922593717 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:240923050C>TN/A show variant in all transcripts IGV

HGNC symbol

NDUFA10

Ensembl transcript ID

ENST00000252711

Genbank transcript ID

NM_004544

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.41770G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1530144

database	homozygous (T/T)	heterozygous	allele carriers
1000G	439	1197	1636
ExAC	5241	16101	21342

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.004	0.004
	-0.341	0.003
(flanking)	-2.099	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

6441

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

102 / 102

chromosome

strand

-1

last intron/exon boundary

1101

theoretical NMD boundary in CDS

949

length of CDS

1068

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)

41770

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

240923050

original gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCGTGGCCCTGACCGTGGGCTCC

altered gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCATGGCCCTGACCGTGGGCTCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALRLLKLAA TSASARVVAA GAQRVRGIHS SVQCKLRYGM WHFLLGDKAS KRLTERSRVI
TVDGNICTGK GKLAKEIAEK LGFKHFPEAG IHYPDSTTGD GKPLATDYNG NCSLEKFYDD
PRSNDGNSYR LQSWLYSSRL LQYSDALEHL LTTGQGVVLE RSIFSDFVFL EAMYNQGFIR
KQCVDHYNEV KSVTICDYLP PHLVIYIDVP VPEVQRRIQK KGDPHEMKIT SAYLQDIENA
YKKTFLPEMS EKCEVLQYSA REAQDSKKVV EDIEYLKFDK GPWLKQDNRT LYHLRLLVQD
KFEVLNYTSI PIFLPEVTIG AHQTDRVLHQ FRELPGRKYS PGYNTEVGDK WIWLK*

mutated AA sequence

N/A

speed

0.68 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999922593717 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:240923050C>TN/A show variant in all transcripts IGV

HGNC symbol

NDUFA10

Ensembl transcript ID

ENST00000404554

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.41770G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1530144

database	homozygous (T/T)	heterozygous	allele carriers
1000G	439	1197	1636
ExAC	5241	16101	21342

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.004	0.004
	-0.341	0.003
(flanking)	-2.099	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

1414

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

6 / 6

chromosome

strand

-1

last intron/exon boundary

1110

theoretical NMD boundary in CDS

1054

length of CDS

1173

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)

41770

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

240923050

original gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCGTGGCCCTGACCGTGGGCTCC

altered gDNA sequence snippet

TGTCAGTGCAGCCTGGCACCATGGCCCTGACCGTGGGCTCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALRLLKLAA TSASARVVAA GAQRVRGIHS SVQCKLRYGM WHFLLGDKAS KRLTERSRVI
TVDGNICTGK GKLAKEIAEK LGFKHFPEAG IHYPDSTTGD GKPLATDYNG NCSLEKFYDD
PRSNDGNSYR LQSWLYSSRL LQYSDALEHL LTTGQGVVLE RSIFSDFVFL EAMYNQGFIR
KQCVDHYNEV KSVTICDYLP PHLVIYIDVP VPEVQRRIQK KGDPHEMKIT SAYLQDIENA
YKKTFLPEMS EKCEVLQYSA REAQDSKKVV EDIEYLKFDK GPWLKQDNRT LYHLRLLVQD
KFEVLNYTSI PIFLPEVTIG AHQTDRVLHQ FRELGIPYPQ RAVQSTREGP EVLLTGLWRW
EDLLIGLQLP GRKYSPGYNT EVGDKWIWLK *

mutated AA sequence

N/A

speed

0.74 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems