MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000458307
Querying Taster for transcript #2: ENST00000273588
Querying Taster for transcript #3: ENST00000395338
Querying Taster for transcript #4: ENST00000538581
Querying Taster for transcript #5: ENST00000546031
MT speed 0 s - this script 4.304773 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AMT	disease_causing_automatic	0.999999999244616	simple_aae		affected	0	R276H	single base exchange	rs121964985		show file
AMT	disease_causing_automatic	0.999999999244616	simple_aae		affected	0	R223H	single base exchange	rs121964985		show file
AMT	disease_causing_automatic	0.999999999833215	simple_aae		affected	0	R320H	single base exchange	rs121964985		show file
AMT	disease_causing_automatic	0.999999999833215	simple_aae		affected	0	R320H	single base exchange	rs121964985		show file
AMT	disease_causing_automatic	0.999999999876055	simple_aae		affected	0	R264H	single base exchange	rs121964985		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999244616 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940064)
known disease mutation: rs11979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49455325C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000458307

Genbank transcript ID

NM_001164710

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.827G>A
cDNA.846G>A
g.4862G>A

AA changes

R276H Score: 29 explain score(s)

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

276

frameshift

known variant

Reference ID: rs121964985

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	9	9

known disease mutation: rs11979 (pathogenic for Non-ketotic hyperglycinemia|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.138	1
	5.189	1
(flanking)	2.902	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	4858	wt: 0.80 / mu: 0.99	wt: AGCGGAGGCGTGTGG mu: AGCGGAGGCATGTGG	CGGA\|ggcg
Donor increased	4863	wt: 0.25 / mu: 0.48	wt: AGGCGTGTGGGGTTG mu: AGGCATGTGGGGTTG	GCGT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

276

mutated

not conserved

276

Ptroglodytes

all identical

ENSPTRG00000014924

320

Mmulatta

all identical

ENSMMUG00000005452

320

Fcatus

all identical

ENSFCAG00000009856

320

Mmusculus

all identical

ENSMUSG00000032607

320

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

330

Drerio

all identical

ENSDARG00000010862

327

Dmelanogaster

all identical

FBgn0032287

318

Celegans

all identical

F25B4.1

316

Xtropicalis

all identical

ENSXETG00000005937

320

protein features

start (aa)	end (aa)	feature	details
273	275	TURN		might get lost (downstream of altered splice site)
283	287	TURN		might get lost (downstream of altered splice site)
289	291	HELIX		might get lost (downstream of altered splice site)
294	299	HELIX		might get lost (downstream of altered splice site)
305	312	HELIX		might get lost (downstream of altered splice site)
319	328	STRAND		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1080 / 1080

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

360 / 360

position of stopcodon in wt / mu cDNA

1099 / 1099

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

20 / 20

chromosome

strand

-1

last intron/exon boundary

921

theoretical NMD boundary in CDS

851

length of CDS

1080

coding sequence (CDS) position

827

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

846

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

4862

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

49455325

original gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

original cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

wildtype AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*

mutated AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRHVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*

speed

0.85 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: 0.999999999244616 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940064)
known disease mutation: rs11979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49455325C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000546031

Genbank transcript ID

N/A

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.668G>A
cDNA.860G>A
g.4862G>A

AA changes

R223H Score: 29 explain score(s)

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

223

frameshift

known variant

Reference ID: rs121964985

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	9	9

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.138	1
	5.189	1
(flanking)	2.902	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	4858	wt: 0.80 / mu: 0.99	wt: AGCGGAGGCGTGTGG mu: AGCGGAGGCATGTGG	CGGA\|ggcg
Donor increased	4863	wt: 0.25 / mu: 0.48	wt: AGGCGTGTGGGGTTG mu: AGGCATGTGGGGTTG	GCGT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

223

mutated

not conserved

223

Ptroglodytes

all identical

ENSPTRG00000014924

320

Mmulatta

all identical

ENSMMUG00000005452

320

Fcatus

all identical

ENSFCAG00000009856

320

Mmusculus

all identical

ENSMUSG00000032607

320

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

330

Drerio

all identical

ENSDARG00000010862

327

Dmelanogaster

all identical

FBgn0032287

318

Celegans

all identical

F25B4.1

316

Xtropicalis

all identical

ENSXETG00000005937

320

protein features

start (aa)	end (aa)	feature	details
215	222	STRAND		might get lost (downstream of altered splice site)
225	235	STRAND		might get lost (downstream of altered splice site)
232	232	BINDING	Substrate.	might get lost (downstream of altered splice site)
237	248	HELIX		might get lost (downstream of altered splice site)
253	255	STRAND		might get lost (downstream of altered splice site)
258	267	HELIX		might get lost (downstream of altered splice site)
261	261	BINDING	Substrate.	might get lost (downstream of altered splice site)
273	275	TURN		might get lost (downstream of altered splice site)
283	287	TURN		might get lost (downstream of altered splice site)
289	291	HELIX		might get lost (downstream of altered splice site)
294	299	HELIX		might get lost (downstream of altered splice site)
305	312	HELIX		might get lost (downstream of altered splice site)
319	328	STRAND		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

921 / 921

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

307 / 307

position of stopcodon in wt / mu cDNA

1113 / 1113

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

193 / 193

chromosome

strand

-1

last intron/exon boundary

935

theoretical NMD boundary in CDS

692

length of CDS

921

coding sequence (CDS) position

668

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

860

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

4862

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

49455325

original gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

original cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

wildtype AA sequence

MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNDI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRRVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*

mutated AA sequence

MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNDI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRHVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*

speed

0.58 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999833215 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940064)
known disease mutation: rs11979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49455325C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000273588

Genbank transcript ID

NM_000481

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.959G>A
cDNA.1262G>A
g.4862G>A

AA changes

R320H Score: 29 explain score(s)

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

320

frameshift

known variant

Reference ID: rs121964985

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	9	9

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.138	1
	5.189	1
(flanking)	2.902	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	4858	wt: 0.80 / mu: 0.99	wt: AGCGGAGGCGTGTGG mu: AGCGGAGGCATGTGG	CGGA\|ggcg
Donor increased	4863	wt: 0.25 / mu: 0.48	wt: AGGCGTGTGGGGTTG mu: AGGCATGTGGGGTTG	GCGT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

320

mutated

not conserved

320

Ptroglodytes

all identical

ENSPTRG00000014924

320

Mmulatta

all identical

ENSMMUG00000005452

320

Fcatus

all identical

ENSFCAG00000009856

320

Mmusculus

all identical

ENSMUSG00000032607

320

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

330

Drerio

all identical

ENSDARG00000010862

327

Dmelanogaster

all identical

FBgn0032287

318

Celegans

all identical

F25B4.1

316

Xtropicalis

all identical

ENSXETG00000005937

320

protein features

start (aa)	end (aa)	feature	details
319	328	STRAND		lost
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1212 / 1212

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

404 / 404

position of stopcodon in wt / mu cDNA

1515 / 1515

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

304 / 304

chromosome

strand

-1

last intron/exon boundary

1337

theoretical NMD boundary in CDS

983

length of CDS

1212

coding sequence (CDS) position

959

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

1262

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

4862

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

49455325

original gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

original cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

wildtype AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*

mutated AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRH VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*

speed

0.62 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999833215 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940064)
known disease mutation: rs11979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49455325C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000395338

Genbank transcript ID

NM_001164712

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.959G>A
cDNA.1187G>A
g.4862G>A

AA changes

R320H Score: 29 explain score(s)

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

320

frameshift

known variant

Reference ID: rs121964985

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	9	9

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.138	1
	5.189	1
(flanking)	2.902	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	4858	wt: 0.80 / mu: 0.99	wt: AGCGGAGGCGTGTGG mu: AGCGGAGGCATGTGG	CGGA\|ggcg
Donor increased	4863	wt: 0.25 / mu: 0.48	wt: AGGCGTGTGGGGTTG mu: AGGCATGTGGGGTTG	GCGT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

320

mutated

not conserved

320

Ptroglodytes

all identical

ENSPTRG00000014924

320

Mmulatta

all identical

ENSMMUG00000005452

320

Fcatus

all identical

ENSFCAG00000009856

320

Mmusculus

all identical

ENSMUSG00000032607

320

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

330

Drerio

all identical

ENSDARG00000010862

327

Dmelanogaster

all identical

FBgn0032287

318

Celegans

all identical

F25B4.1

316

Xtropicalis

all identical

ENSXETG00000005937

320

protein features

start (aa)	end (aa)	feature	details
319	328	STRAND		lost
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1161 / 1161

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

387 / 387

position of stopcodon in wt / mu cDNA

1389 / 1389

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

229 / 229

chromosome

strand

-1

last intron/exon boundary

1366

theoretical NMD boundary in CDS

1087

length of CDS

1161

coding sequence (CDS) position

959

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

1187

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

4862

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

49455325

original gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

original cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

wildtype AA sequence

mutated AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRH VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEL PSGPCF*

speed

0.75 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999876055 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940064)
known disease mutation: rs11979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49455325C>TN/A show variant in all transcripts IGV

HGNC symbol

AMT

Ensembl transcript ID

ENST00000538581

Genbank transcript ID

NM_001164711

UniProt peptide

P48728

alteration type

single base exchange

alteration region

CDS

DNA changes

c.791G>A
cDNA.1019G>A
g.4862G>A

AA changes

R264H Score: 29 explain score(s)

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

264

frameshift

known variant

Reference ID: rs121964985

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	9	9

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.138	1
	5.189	1
(flanking)	2.902	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	4858	wt: 0.80 / mu: 0.99	wt: AGCGGAGGCGTGTGG mu: AGCGGAGGCATGTGG	CGGA\|ggcg
Donor increased	4863	wt: 0.25 / mu: 0.48	wt: AGGCGTGTGGGGTTG mu: AGGCATGTGGGGTTG	GCGT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

264

mutated

not conserved

264

Ptroglodytes

all identical

ENSPTRG00000014924

320

Mmulatta

all identical

ENSMMUG00000005452

320

Fcatus

all identical

ENSFCAG00000009856

320

Mmusculus

all identical

ENSMUSG00000032607

320

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

330

Drerio

all identical

ENSDARG00000010862

327

Dmelanogaster

all identical

FBgn0032287

318

Celegans

all identical

F25B4.1

316

Xtropicalis

all identical

ENSXETG00000005937

320

protein features

start (aa)	end (aa)	feature	details
258	267	HELIX		lost
273	275	TURN		might get lost (downstream of altered splice site)
283	287	TURN		might get lost (downstream of altered splice site)
289	291	HELIX		might get lost (downstream of altered splice site)
294	299	HELIX		might get lost (downstream of altered splice site)
305	312	HELIX		might get lost (downstream of altered splice site)
319	328	STRAND		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
343	353	STRAND		might get lost (downstream of altered splice site)
354	357	TURN		might get lost (downstream of altered splice site)
358	365	STRAND		might get lost (downstream of altered splice site)
367	369	HELIX		might get lost (downstream of altered splice site)
375	380	STRAND		might get lost (downstream of altered splice site)
383	390	STRAND		might get lost (downstream of altered splice site)
399	399	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1044 / 1044

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

348 / 348

position of stopcodon in wt / mu cDNA

1272 / 1272

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

229 / 229

chromosome

strand

-1

last intron/exon boundary

1094

theoretical NMD boundary in CDS

815

length of CDS

1044

coding sequence (CDS) position

791

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

1019

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

4862

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

49455325

original gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered gDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

original cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG

altered cDNA sequence snippet

GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG

wildtype AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGND IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*

mutated AA sequence

MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGND IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRHVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*

speed

0.42 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

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems