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: ENST00000371694
Querying Taster for transcript #2: ENST00000371696
Querying Taster for transcript #3: ENST00000538402
MT speed 0 s - this script 3.884352 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGPAT2	disease_causing_automatic	0.999999999951448	simple_aae		affected	0	L228P	single base exchange	rs104894100		show file
AGPAT2	disease_causing_automatic	0.999999999951448	simple_aae		affected	0	L196P	single base exchange	rs104894100		show file
AGPAT2	disease_causing_automatic	0.999999999951448	simple_aae		affected	0	L228P	single base exchange	rs104894100		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999951448 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020920)
known disease mutation: rs6627 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:139568358A>GN/A show variant in all transcripts IGV

HGNC symbol

AGPAT2

Ensembl transcript ID

ENST00000371696

Genbank transcript ID

NM_006412

UniProt peptide

O15120

alteration type

single base exchange

alteration region

CDS

DNA changes

c.683T>C
cDNA.749T>C
g.13518T>C

AA changes

L228P Score: 98 explain score(s)

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

228

frameshift

known variant

Reference ID: rs104894100
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs6627 (pathogenic for Congenital generalized lipodystrophy type 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM020920)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020920)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020920)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
Cmyc, Transcription Factor, Cmyc TF binding
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.234	0.997
	1.686	1
(flanking)	2.543	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 increased	13517	wt: 0.57 / mu: 0.69	wt: AGGTGCTGGAAGCCA mu: AGGTGCCGGAAGCCA	GTGC\|tgga
Donor increased	13522	wt: 0.70 / mu: 0.86	wt: CTGGAAGCCATCCCC mu: CCGGAAGCCATCCCC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

228

mutated

not conserved

228

Ptroglodytes

all identical

ENSPTRG00000021564

167

Mmulatta

all identical

ENSMMUG00000020990

229

Fcatus

all identical

ENSFCAG00000011607

167

Mmusculus

all identical

ENSMUSG00000026922

228

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018530

231

Drerio

all identical

ENSDARG00000068437

227

Dmelanogaster

all identical

FBgn0030421

233

Celegans

all identical

T06E8.1

228

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
255	255	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
260	260	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

837 / 837

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

279 / 279

position of stopcodon in wt / mu cDNA

903 / 903

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

728

theoretical NMD boundary in CDS

611

length of CDS

837

coding sequence (CDS) position

683

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

749

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

13518

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

139568358

original gDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered gDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

original cDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered cDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

wildtype AA sequence

MELWPCLAAA LLLLLLLVQL SRAAEFYAKV ALYCALCFTV SAVASLVCLL RHGGRTVENM
SIIGWFVRSF KYFYGLRFEV RDPRRLQEAR PCVIVSNHQS ILDMMGLMEV LPERCVQIAK
RELLFLGPVG LIMYLGGVFF INRQRSSTAM TVMADLGERM VRENLKVWIY PEGTRNDNGD
LLPFKKGAFY LAVQAQVPIV PVVYSSFSSF YNTKKKFFTS GTVTVQVLEA IPTSGLTAAD
VPALVDTCHR AMRTTFLHIS KTPQENGATA GSGVQPAQ*

mutated AA sequence

MELWPCLAAA LLLLLLLVQL SRAAEFYAKV ALYCALCFTV SAVASLVCLL RHGGRTVENM
SIIGWFVRSF KYFYGLRFEV RDPRRLQEAR PCVIVSNHQS ILDMMGLMEV LPERCVQIAK
RELLFLGPVG LIMYLGGVFF INRQRSSTAM TVMADLGERM VRENLKVWIY PEGTRNDNGD
LLPFKKGAFY LAVQAQVPIV PVVYSSFSSF YNTKKKFFTS GTVTVQVPEA IPTSGLTAAD
VPALVDTCHR AMRTTFLHIS KTPQENGATA GSGVQPAQ*

speed

0.90 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: 0.999999999951448 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020920)
known disease mutation: rs6627 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:139568358A>GN/A show variant in all transcripts IGV

HGNC symbol

AGPAT2

Ensembl transcript ID

ENST00000371694

Genbank transcript ID

NM_001012727

UniProt peptide

O15120

alteration type

single base exchange

alteration region

CDS

DNA changes

c.587T>C
cDNA.628T>C
g.13518T>C

AA changes

L196P Score: 98 explain score(s)

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

196

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.234	0.997
	1.686	1
(flanking)	2.543	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 increased	13517	wt: 0.57 / mu: 0.69	wt: AGGTGCTGGAAGCCA mu: AGGTGCCGGAAGCCA	GTGC\|tgga
Donor increased	13522	wt: 0.70 / mu: 0.86	wt: CTGGAAGCCATCCCC mu: CCGGAAGCCATCCCC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

196

mutated

not conserved

196

Ptroglodytes

all identical

ENSPTRG00000021564

152

Mmulatta

all identical

ENSMMUG00000020990

212

Fcatus

all identical

ENSFCAG00000011607

152

Mmusculus

all identical

ENSMUSG00000026922

212

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018530

225

Drerio

all identical

ENSDARG00000068437

225

Dmelanogaster

all identical

FBgn0030421

229

Celegans

all identical

T06E8.1

223

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
200	200	CONFLICT	V -> F (in Ref. 7; AAH00026).	might get lost (downstream of altered splice site)
255	255	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
260	260	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

741 / 741

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

247 / 247

position of stopcodon in wt / mu cDNA

782 / 782

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

42 / 42

chromosome

strand

-1

last intron/exon boundary

607

theoretical NMD boundary in CDS

515

length of CDS

741

coding sequence (CDS) position

587

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

628

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

13518

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

139568358

original gDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered gDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

original cDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered cDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

wildtype AA sequence

MELWPCLAAA LLLLLLLVQL SRAAEFYAKV ALYCALCFTV SAVASLVCLL RHGGRTVENM
SIIGWFVRSF KYFYGLRFEV RDPRRLQEAR PCVIVSNHQS ILDMMGLMEV LPERCVQIAK
RELLFLGPVG LIMYLGGVFF INRQRSSTAM TVMADLGERM VRENVPIVPV VYSSFSSFYN
TKKKFFTSGT VTVQVLEAIP TSGLTAADVP ALVDTCHRAM RTTFLHISKT PQENGATAGS
GVQPAQ*

mutated AA sequence

MELWPCLAAA LLLLLLLVQL SRAAEFYAKV ALYCALCFTV SAVASLVCLL RHGGRTVENM
SIIGWFVRSF KYFYGLRFEV RDPRRLQEAR PCVIVSNHQS ILDMMGLMEV LPERCVQIAK
RELLFLGPVG LIMYLGGVFF INRQRSSTAM TVMADLGERM VRENVPIVPV VYSSFSSFYN
TKKKFFTSGT VTVQVPEAIP TSGLTAADVP ALVDTCHRAM RTTFLHISKT PQENGATAGS
GVQPAQ*

speed

0.81 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999951448 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020920)
known disease mutation: rs6627 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:139568358A>GN/A show variant in all transcripts IGV

HGNC symbol

AGPAT2

Ensembl transcript ID

ENST00000538402

Genbank transcript ID

N/A

UniProt peptide

O15120

alteration type

single base exchange

alteration region

CDS

DNA changes

c.683T>C
cDNA.722T>C
g.13518T>C

AA changes

L228P Score: 98 explain score(s)

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

228

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.234	0.997
	1.686	1
(flanking)	2.543	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 increased	13517	wt: 0.57 / mu: 0.69	wt: AGGTGCTGGAAGCCA mu: AGGTGCCGGAAGCCA	GTGC\|tgga
Donor increased	13522	wt: 0.70 / mu: 0.86	wt: CTGGAAGCCATCCCC mu: CCGGAAGCCATCCCC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

228

mutated

not conserved

228

Ptroglodytes

all identical

ENSPTRG00000021564

167

Mmulatta

all identical

ENSMMUG00000020990

229

Fcatus

all identical

ENSFCAG00000011607

167

Mmusculus

all identical

ENSMUSG00000026922

228

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018530

231

Drerio

all identical

ENSDARG00000068437

227

Dmelanogaster

all identical

FBgn0030421

233

Celegans

all identical

T06E8.1

228

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
255	255	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
260	260	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

837 / 837

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

279 / 279

position of stopcodon in wt / mu cDNA

876 / 876

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

40 / 40

chromosome

strand

-1

last intron/exon boundary

1229

theoretical NMD boundary in CDS

1139

length of CDS

837

coding sequence (CDS) position

683

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

722

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

13518

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

139568358

original gDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered gDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

original cDNA sequence snippet

AACAGTCACAGTGCAGGTGCTGGAAGCCATCCCCACCAGCG

altered cDNA sequence snippet

AACAGTCACAGTGCAGGTGCCGGAAGCCATCCCCACCAGCG

wildtype AA sequence

mutated AA sequence

MELWPCLAAA LLLLLLLVQL SRAAEFYAKV ALYCALCFTV SAVASLVCLL RHGGRTVENM
SIIGWFVRSF KYFYGLRFEV RDPRRLQEAR PCVIVSNHQS ILDMMGLMEV LPERCVQIAK
RELLFLGPVG LIMYLGGVFF INRQRSSTAM TVMADLGERM VRENLKVWIY PEGTRNDNGD
LLPFKKGAFY LAVQAQVPIV PVVYSSFSSF YNTKKKFFTS GTVTVQVPEA IPTSGLTAAD
VPALVDTCHR AMRTTFLHIS KTPQENGATA GSGVQPAQ*

speed

0.95 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