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 5.456463 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AMT	disease_causing_automatic	0.999999999953032	simple_aae		affected	0	G47R	single base exchange	rs121964982		show file
AMT	disease_causing_automatic	0.999999999953032	simple_aae		affected	0	G47R	single base exchange	rs121964982		show file
AMT	disease_causing_automatic	0.999999999953032	simple_aae		affected	0	G47R	single base exchange	rs121964982		show file
AMT	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121964982		show file
AMT	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121964982		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999953032 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>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.139G>A
cDNA.158G>A
g.531G>A

AA changes

G47R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

known disease mutation: rs11975 (pathogenic for Non-ketotic hyperglycinemia|Inborn genetic diseases) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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
Acc marginally increased	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000014924

Mmulatta

all identical

ENSMMUG00000005452

Fcatus

all identical

ENSFCAG00000009856

Mmusculus

all identical

ENSMUSG00000032607

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

Drerio

all identical

ENSDARG00000010862

Dmelanogaster

all identical

FBgn0032287

Celegans

all identical

F25B4.1

Xtropicalis

all identical

ENSXETG00000005937

protein features

start (aa)	end (aa)	feature	details
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
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

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

139

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

158

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

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered cDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

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 FHLAHGRKMV 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*

speed

1.08 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: 0.999999999953032 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>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.139G>A
cDNA.442G>A
g.531G>A

AA changes

G47R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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
Acc marginally increased	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000014924

Mmulatta

all identical

ENSMMUG00000005452

Fcatus

all identical

ENSFCAG00000009856

Mmusculus

all identical

ENSMUSG00000032607

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

Drerio

all identical

ENSDARG00000010862

Dmelanogaster

all identical

FBgn0032287

Celegans

all identical

F25B4.1

Xtropicalis

all identical

ENSXETG00000005937

protein features

start (aa)	end (aa)	feature	details
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
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

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

139

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

442

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

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered cDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

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 FHLAHGRKMV 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*

speed

1.11 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999953032 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>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.139G>A
cDNA.367G>A
g.531G>A

AA changes

G47R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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
Acc marginally increased	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000014924

Mmulatta

all identical

ENSMMUG00000005452

Fcatus

all identical

ENSFCAG00000009856

Mmusculus

all identical

ENSMUSG00000032607

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008892

Drerio

all identical

ENSDARG00000010862

Dmelanogaster

all identical

FBgn0032287

Celegans

all identical

F25B4.1

Xtropicalis

all identical

ENSXETG00000005937

protein features

start (aa)	end (aa)	feature	details
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
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

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

139

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

367

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

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered cDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

wildtype AA sequence

mutated AA sequence

speed

1.12 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 CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>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

intron

DNA changes

g.531G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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
Acc marginally increased	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

138

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
39	44	HELIX		might get lost (downstream of altered splice site)
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
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

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

229 / 229

chromosome

strand

-1

last intron/exon boundary

1094

theoretical NMD boundary in CDS

815

length of CDS

1044

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)

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

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

N/A

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 CM060825)
known disease mutation at this position (HGMD CM940062)
known disease mutation: rs11975 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:49459656C>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

intron

DNA changes

g.531G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121964982

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.76	1
	5.412	1
(flanking)	-1.765	0.355

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

splice sites

splice site change before start ATG (at aa -33) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	532	wt: 0.4473 / mu: 0.4763 (marginal change - not scored)	wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG	gcgg\|GAAA
Acc marginally increased	522	wt: 0.2275 / mu: 0.2275 (marginal change - not scored)	wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG	ctgg\|CCCA
Donor increased	532	wt: 0.43 / mu: 0.87	wt: CGGCGGGAAAATGGT mu: CGGCAGGAAAATGGT	GCGG\|gaaa
Donor increased	531	wt: 0.66 / mu: 0.97	wt: ACGGCGGGAAAATGG mu: ACGGCAGGAAAATGG	GGCG\|ggaa
Donor gained	527	0.69	mu: GCCCACGGCAGGAAA	CCAC\|ggca

distance from splice site

138

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	TRANSIT	Mitochondrion (By similarity).	might get lost (downstream of altered splice site)
39	44	HELIX		might get lost (downstream of altered splice site)
48	52	STRAND		might get lost (downstream of altered splice site)
55	60	STRAND		might get lost (downstream of altered splice site)
65	74	HELIX		might get lost (downstream of altered splice site)
75	80	STRAND		might get lost (downstream of altered splice site)
84	91	STRAND		might get lost (downstream of altered splice site)
94	101	HELIX		might get lost (downstream of altered splice site)
95	95	CONFLICT	V -> C (in Ref. 2; BAA03512).	might get lost (downstream of altered splice site)
102	104	STRAND		might get lost (downstream of altered splice site)
113	120	STRAND		might get lost (downstream of altered splice site)
126	134	STRAND		might get lost (downstream of altered splice site)
138	144	STRAND		might get lost (downstream of altered splice site)
146	148	HELIX		might get lost (downstream of altered splice site)
149	165	HELIX		might get lost (downstream of altered splice site)
171	174	STRAND		might get lost (downstream of altered splice site)
178	184	STRAND		might get lost (downstream of altered splice site)
187	192	HELIX		might get lost (downstream of altered splice site)
199	201	HELIX		might get lost (downstream of altered splice site)
206	212	STRAND		might get lost (downstream of altered splice site)
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

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

193 / 193

chromosome

strand

-1

last intron/exon boundary

935

theoretical NMD boundary in CDS

692

length of CDS

921

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)

531

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

49459656

original gDNA sequence snippet

ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG

altered gDNA sequence snippet

ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

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

N/A

speed

0.93 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