MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000373925
Querying Taster for transcript #2: ENST00000373927
Querying Taster for transcript #3: ENST00000373921
Querying Taster for transcript #4: ENST00000328928
MT speed 0 s - this script 4.693592 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
THEMIS2	polymorphism_automatic	4.37723090596087e-06	simple_aae				K511E	single base exchange	rs3766400		show file
THEMIS2	polymorphism_automatic	4.37723090596087e-06	simple_aae				K382E	single base exchange	rs3766400		show file
THEMIS2	polymorphism_automatic	0.999982557077538	without_aae					single base exchange	rs3766400		show file
THEMIS2	polymorphism_automatic	0.999982557077538	without_aae					single base exchange	rs3766400		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999995622769094 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:28209366A>GN/A show variant in all transcripts IGV

HGNC symbol

THEMIS2

Ensembl transcript ID

ENST00000373921

Genbank transcript ID

NM_001105556

UniProt peptide

Q5TEJ8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1531A>G
cDNA.1535A>G
g.10312A>G

AA changes

K511E Score: 56 explain score(s)

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

511

frameshift

known variant

Reference ID: rs3766400

database	homozygous (G/G)	heterozygous	allele carriers
1000G	662	932	1594
ExAC	21689	-10611	11078

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.469	0.925
	0.721	0.666
(flanking)	0.391	0.286

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

189

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

511

mutated

all conserved

511

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000018170

511

Fcatus

no alignment

ENSFCAG00000003404

n/a

Mmusculus

all conserved

ENSMUSG00000037731

512

Ggallus

not conserved

ENSGALG00000000731

440

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
239	514	REGION	CABIT 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1932 / 1932

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

644 / 644

position of stopcodon in wt / mu cDNA

1936 / 1936

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

5 / 5

chromosome

strand

last intron/exon boundary

1881

theoretical NMD boundary in CDS

1826

length of CDS

1932

coding sequence (CDS) position

1531

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

1535

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

10312

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

28209366

original gDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered gDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

original cDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered cDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

wildtype AA sequence

MEPVPLQDFV RALDPASLPR VLRVCSGVYF EGSIYEISGN ECCLSTGDLI KVTQVRLQKV
VCENPKTSQT MELAPNFQGY FTPLNTPQSY ETLEELVSAT TQSSKQLPTC FMSTHRIVTE
GRVVTEDQLL MLEAVVMHLG IRSARCVLGM EGQQVILHLP LSQKGPFWTW EPSAPRTLLQ
VLQDPALKDL VLTCPTLPWH SLILRPQYEI QAIMHMRRTI VKIPSTLEVD VEDVTASSRH
VHFIKPLLLS EVLAWEGPFP LSMEILEVPE GRPIFLSPWV GSLQKGQRLC VYGLASPPWR
VLASSKGRKV PRHFLVSGGY QGKLRRRPRE FPTAYDLLGA FQPGRPLRVV ATKDCEGERE
ENPEFTSLAV GDRLEVLGPG QAHGAQGSDV DVLVCQRLSD QAGEDEEEEC KEEAESPERV
LLPFHFPGSF VEEMSDSRRY SLADLTAQFS LPCEVKVVAK DTSHPTDPLT SFLGLRLEEK
ITEPFLVVSL DSEPGMCFEI PPRWLDLTVV KAKGQPDLPE GSLPIATVEE LTDTFYYRLR
KLPACEIQAP PPRPPKNQGL SKQRRHSSEG GVKSSQVLGL QQHARLPKPK AKTLPEFIKD
GSSTYSKIPA HRKGHRPAKP QRQDLDDDEH DYEEILEQFQ KTI*

mutated AA sequence

MEPVPLQDFV RALDPASLPR VLRVCSGVYF EGSIYEISGN ECCLSTGDLI KVTQVRLQKV
VCENPKTSQT MELAPNFQGY FTPLNTPQSY ETLEELVSAT TQSSKQLPTC FMSTHRIVTE
GRVVTEDQLL MLEAVVMHLG IRSARCVLGM EGQQVILHLP LSQKGPFWTW EPSAPRTLLQ
VLQDPALKDL VLTCPTLPWH SLILRPQYEI QAIMHMRRTI VKIPSTLEVD VEDVTASSRH
VHFIKPLLLS EVLAWEGPFP LSMEILEVPE GRPIFLSPWV GSLQKGQRLC VYGLASPPWR
VLASSKGRKV PRHFLVSGGY QGKLRRRPRE FPTAYDLLGA FQPGRPLRVV ATKDCEGERE
ENPEFTSLAV GDRLEVLGPG QAHGAQGSDV DVLVCQRLSD QAGEDEEEEC KEEAESPERV
LLPFHFPGSF VEEMSDSRRY SLADLTAQFS LPCEVKVVAK DTSHPTDPLT SFLGLRLEEK
ITEPFLVVSL DSEPGMCFEI PPRWLDLTVV EAKGQPDLPE GSLPIATVEE LTDTFYYRLR
KLPACEIQAP PPRPPKNQGL SKQRRHSSEG GVKSSQVLGL QQHARLPKPK AKTLPEFIKD
GSSTYSKIPA HRKGHRPAKP QRQDLDDDEH DYEEILEQFQ KTI*

speed

1.11 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: simple_aae, prob: 0.999995622769094 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:28209366A>GN/A show variant in all transcripts IGV

HGNC symbol

THEMIS2

Ensembl transcript ID

ENST00000328928

Genbank transcript ID

N/A

UniProt peptide

Q5TEJ8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1144A>G
cDNA.1172A>G
g.10312A>G

AA changes

K382E Score: 56 explain score(s)

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

382

frameshift

known variant

Reference ID: rs3766400

database	homozygous (G/G)	heterozygous	allele carriers
1000G	662	932	1594
ExAC	21689	-10611	11078

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.469	0.925
	0.721	0.666
(flanking)	0.391	0.286

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

189

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

382

mutated

all conserved

382

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000018170

511

Fcatus

no alignment

ENSFCAG00000003404

n/a

Mmusculus

all conserved

ENSMUSG00000037731

512

Ggallus

not conserved

ENSGALG00000000731

440

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
239	514	REGION	CABIT 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1545 / 1545

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

515 / 515

position of stopcodon in wt / mu cDNA

1573 / 1573

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

29 / 29

chromosome

strand

last intron/exon boundary

1518

theoretical NMD boundary in CDS

1439

length of CDS

1545

coding sequence (CDS) position

1144

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

1172

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

10312

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

28209366

original gDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered gDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

original cDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered cDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

wildtype AA sequence

MEPVPLQDFV RALDPASLPR VLRVCSGVYF EGSIYEISGN ECCLSTGDLI KVTQVRLQKV
VCENPKTSQT MELAPNFQGY FTPLNTPQSY ETLEELVSAT TQSSKQLPTC FMSTHRIVTE
GRVVTEDQLL MLEAVVMHLG IRSARCVLGM EGQQVILHLP LSQKGPFWTW EPSAPRTLLQ
VLQDPALKDL VLTCPTLPWH SLILRPQYEI QAIMHMRRTI VKIPSTLEVD VEDVTASSRH
VHFIKPLLLS EVLAWEGPFP LSMEILERLS DQAGEDEEEE CKEEAESPER VLLPFHFPGS
FVEEMSDSRR YSLADLTAQF SLPCEVKVVA KDTSHPTDPL TSFLGLRLEE KITEPFLVVS
LDSEPGMCFE IPPRWLDLTV VKAKGQPDLP EGSLPIATVE ELTDTFYYRL RKLPACEIQA
PPPRPPKNQG LSKQRRHSSE GGVKSSQVLG LQQHARLPKP KAKTLPEFIK DGSSTYSKIP
AHRKGHRPAK PQRQDLDDDE HDYEEILEQF QKTI*

mutated AA sequence

MEPVPLQDFV RALDPASLPR VLRVCSGVYF EGSIYEISGN ECCLSTGDLI KVTQVRLQKV
VCENPKTSQT MELAPNFQGY FTPLNTPQSY ETLEELVSAT TQSSKQLPTC FMSTHRIVTE
GRVVTEDQLL MLEAVVMHLG IRSARCVLGM EGQQVILHLP LSQKGPFWTW EPSAPRTLLQ
VLQDPALKDL VLTCPTLPWH SLILRPQYEI QAIMHMRRTI VKIPSTLEVD VEDVTASSRH
VHFIKPLLLS EVLAWEGPFP LSMEILERLS DQAGEDEEEE CKEEAESPER VLLPFHFPGS
FVEEMSDSRR YSLADLTAQF SLPCEVKVVA KDTSHPTDPL TSFLGLRLEE KITEPFLVVS
LDSEPGMCFE IPPRWLDLTV VEAKGQPDLP EGSLPIATVE ELTDTFYYRL RKLPACEIQA
PPPRPPKNQG LSKQRRHSSE GGVKSSQVLG LQQHARLPKP KAKTLPEFIK DGSSTYSKIP
AHRKGHRPAK PQRQDLDDDE HDYEEILEQF QKTI*

speed

0.77 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 1.74429224620363e-05 (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)

chr1:28209366A>GN/A show variant in all transcripts IGV

HGNC symbol

THEMIS2

Ensembl transcript ID

ENST00000373927

Genbank transcript ID

NM_001039477

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.10312A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3766400

database	homozygous (G/G)	heterozygous	allele carriers
1000G	662	932	1594
ExAC	21689	-10611	11078

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.469	0.925
	0.721	0.666
(flanking)	0.391	0.286

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

2440

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

24 / 24

chromosome

strand

last intron/exon boundary

416

theoretical NMD boundary in CDS

342

length of CDS

372

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)

10312

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

28209366

original gDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered gDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEPVPLQDFV RALDPASLPR VLRVCSGVYF EGSIYEISGN ECCLSTGDLI KVTQVRLQKV
VCENPKTSQT MELAPNFQVF SSLRIAATRS AAQTQGEDLA RVHQGWLQYV QQDSCPQEGP
QAR*

mutated AA sequence

N/A

speed

0.87 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 1.74429224620363e-05 (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)

chr1:28209366A>GN/A show variant in all transcripts IGV

HGNC symbol

THEMIS2

Ensembl transcript ID

ENST00000373925

Genbank transcript ID

NM_004848

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.10312A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3766400

database	homozygous (G/G)	heterozygous	allele carriers
1000G	662	932	1594
ExAC	21689	-10611	11078

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.469	0.925
	0.721	0.666
(flanking)	0.391	0.286

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

2440

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

29 / 29

chromosome

strand

last intron/exon boundary

832

theoretical NMD boundary in CDS

753

length of CDS

783

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)

10312

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

28209366

original gDNA sequence snippet

GGCTGGACCTGACTGTTGTGAAGGCCAAGGGGCAGCCAGAC

altered gDNA sequence snippet

GGCTGGACCTGACTGTTGTGGAGGCCAAGGGGCAGCCAGAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.62 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems