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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000352480
Querying Taster for transcript #2: ENST00000372394
Querying Taster for transcript #3: ENST00000372393
Querying Taster for transcript #4: ENST00000334909
MT speed 0 s - this script 8.750581 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ASS1	disease_causing_automatic	0.999998782306832	simple_aae			0	S180N	single base exchange	rs121908638		show file
ASS1	disease_causing_automatic	0.999998782306832	simple_aae			0	S180N	single base exchange	rs121908638		show file
ASS1	disease_causing_automatic	0.999998782306832	simple_aae			0	S180N	single base exchange	rs121908638		show file
ASS1	disease_causing_automatic	0.999998782306832	simple_aae			0	S180N	single base exchange	rs121908638		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998782306832 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM146379)
known disease mutation at this position (HGMD CM900033)
known disease mutation: rs6326 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133346264G>AN/A show variant in all transcripts IGV

HGNC symbol

ASS1

Ensembl transcript ID

ENST00000352480

Genbank transcript ID

NM_054012

UniProt peptide

P00966

alteration type

single base exchange

alteration region

CDS

DNA changes

c.539G>A
cDNA.611G>A
g.26171G>A

AA changes

S180N Score: 46 explain score(s)

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

180

frameshift

known variant

Reference ID: rs121908638

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs6326 (pathogenic for Citrullinemia type I|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900033)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM146379)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM146379)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900033)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.375	1
	2.579	1
(flanking)	0.654	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 marginally increased	26175	wt: 0.9549 / mu: 0.9812 (marginal change - not scored)	wt: AGCATGGATGAGAAC mu: AACATGGATGAGAAC	CATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

180

mutated

all conserved

180

Ptroglodytes

all identical

ENSPTRG00000021473

180

Mmulatta

all identical

ENSMMUG00000019199

180

Fcatus

not conserved

ENSFCAG00000005111

180

Mmusculus

all identical

ENSMUSG00000046687

180

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

179

Drerio

all identical

ENSDARG00000032564

Dmelanogaster

all identical

FBgn0026565

179

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

181

protein features

start (aa)	end (aa)	feature	details
180	180	BINDING	Citrulline.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1311 / 1311

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

73 / 73

chromosome

strand

last intron/exon boundary

1266

theoretical NMD boundary in CDS

1143

length of CDS

1239

coding sequence (CDS) position

539

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

611

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

26171

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

133346264

original gDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered gDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

original cDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered cDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

wildtype AA sequence

MSSKGSVVLA YSGGLDTSCI LVWLKEQGYD VIAYLANIGQ KEDFEEARKK ALKLGAKKVF
IEDVSREFVE EFIWPAIQSS ALYEDRYLLG TSLARPCIAR KQVEIAQREG AKYVSHGATG
KGNDQVRFEL SCYSLAPQIK VIAPWRMPEF YNRFKGRNDL MEYAKQHGIP IPVTPKNPWS
MDENLMHISY EAGILENPKN QAPPGLYTKT QDPAKAPNTP DILEIEFKKG VPVKVTNVKD
GTTHQTSLEL FMYLNEVAGK HGVGRIDIVE NRFIGMKSRG IYETPAGTIL YHAHLDIEAF
TMDREVRKIK QGLGLKFAEL VYTGFWHSPE CEFVRHCIAK SQERVEGKVQ VSVLKGQVYI
LGRESPLSLY NEELVSMNVQ GDYEPTDATG FININSLRLK EYHRLQSKVT AK*

mutated AA sequence

MSSKGSVVLA YSGGLDTSCI LVWLKEQGYD VIAYLANIGQ KEDFEEARKK ALKLGAKKVF
IEDVSREFVE EFIWPAIQSS ALYEDRYLLG TSLARPCIAR KQVEIAQREG AKYVSHGATG
KGNDQVRFEL SCYSLAPQIK VIAPWRMPEF YNRFKGRNDL MEYAKQHGIP IPVTPKNPWN
MDENLMHISY EAGILENPKN QAPPGLYTKT QDPAKAPNTP DILEIEFKKG VPVKVTNVKD
GTTHQTSLEL FMYLNEVAGK HGVGRIDIVE NRFIGMKSRG IYETPAGTIL YHAHLDIEAF
TMDREVRKIK QGLGLKFAEL VYTGFWHSPE CEFVRHCIAK SQERVEGKVQ VSVLKGQVYI
LGRESPLSLY NEELVSMNVQ GDYEPTDATG FININSLRLK EYHRLQSKVT AK*

speed

0.13 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: 0.999998782306832 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM146379)
known disease mutation at this position (HGMD CM900033)
known disease mutation: rs6326 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133346264G>AN/A show variant in all transcripts IGV

HGNC symbol

ASS1

Ensembl transcript ID

ENST00000372394

Genbank transcript ID

N/A

UniProt peptide

P00966

alteration type

single base exchange

alteration region

CDS

DNA changes

c.539G>A
cDNA.1020G>A
g.26171G>A

AA changes

S180N Score: 46 explain score(s)

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

180

frameshift

known variant

Reference ID: rs121908638

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.375	1
	2.579	1
(flanking)	0.654	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 marginally increased	26175	wt: 0.9549 / mu: 0.9812 (marginal change - not scored)	wt: AGCATGGATGAGAAC mu: AACATGGATGAGAAC	CATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

180

mutated

all conserved

180

Ptroglodytes

all identical

ENSPTRG00000021473

180

Mmulatta

all identical

ENSMMUG00000019199

180

Fcatus

not conserved

ENSFCAG00000005111

180

Mmusculus

all identical

ENSMUSG00000046687

180

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

179

Drerio

all identical

ENSDARG00000032564

Dmelanogaster

all identical

FBgn0026565

179

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

181

protein features

start (aa)	end (aa)	feature	details
180	180	BINDING	Citrulline.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1720 / 1720

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

482 / 482

chromosome

strand

last intron/exon boundary

1675

theoretical NMD boundary in CDS

1143

length of CDS

1239

coding sequence (CDS) position

539

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

1020

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

26171

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

133346264

original gDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered gDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

original cDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered cDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

wildtype AA sequence

mutated AA sequence

MSSKGSVVLA YSGGLDTSCI LVWLKEQGYD VIAYLANIGQ KEDFEEARKK ALKLGAKKVF
IEDVSREFVE EFIWPAIQSS ALYEDRYLLG TSLARPCIAR KQVEIAQREG AKYVSHGATG
KGNDQVRFEL SCYSLAPQIK VIAPWRMPEF YNRFKGRNDL MEYAKQHGIP IPVTPKNPWN
MDENLMHISY EAGILENPKN QAPPGLYTKT QDPAKAPNTP DILEIEFKKG VPVKVTNVKD
GTTHQTSLEL FMYLNEVAGK HGVGRIDIVE NRFIGMKSRG IYETPAGTIL YHAHLDIEAF
TMDREVRKIK QGLGLKFAEL VYTGFWHSPE CEFVRHCIAK SQERVEGKVQ VSVLKGQVYI
LGRESPLSLY NEELVSMNVQ GDYEPTDATG FININSLRLK EYHRLQSKVT AK*

speed

1.36 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998782306832 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM146379)
known disease mutation at this position (HGMD CM900033)
known disease mutation: rs6326 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133346264G>AN/A show variant in all transcripts IGV

HGNC symbol

ASS1

Ensembl transcript ID

ENST00000372393

Genbank transcript ID

N/A

UniProt peptide

P00966

alteration type

single base exchange

alteration region

CDS

DNA changes

c.539G>A
cDNA.612G>A
g.26171G>A

AA changes

S180N Score: 46 explain score(s)

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

180

frameshift

known variant

Reference ID: rs121908638

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.375	1
	2.579	1
(flanking)	0.654	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 marginally increased	26175	wt: 0.9549 / mu: 0.9812 (marginal change - not scored)	wt: AGCATGGATGAGAAC mu: AACATGGATGAGAAC	CATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

180

mutated

all conserved

180

Ptroglodytes

all identical

ENSPTRG00000021473

180

Mmulatta

all identical

ENSMMUG00000019199

180

Fcatus

not conserved

ENSFCAG00000005111

180

Mmusculus

all identical

ENSMUSG00000046687

180

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

179

Drerio

all identical

ENSDARG00000032564

Dmelanogaster

all identical

FBgn0026565

179

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

181

protein features

start (aa)	end (aa)	feature	details
180	180	BINDING	Citrulline.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1312 / 1312

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

74 / 74

chromosome

strand

last intron/exon boundary

1267

theoretical NMD boundary in CDS

1143

length of CDS

1239

coding sequence (CDS) position

539

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

612

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

26171

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

133346264

original gDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered gDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

original cDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered cDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

wildtype AA sequence

mutated AA sequence

MSSKGSVVLA YSGGLDTSCI LVWLKEQGYD VIAYLANIGQ KEDFEEARKK ALKLGAKKVF
IEDVSREFVE EFIWPAIQSS ALYEDRYLLG TSLARPCIAR KQVEIAQREG AKYVSHGATG
KGNDQVRFEL SCYSLAPQIK VIAPWRMPEF YNRFKGRNDL MEYAKQHGIP IPVTPKNPWN
MDENLMHISY EAGILENPKN QAPPGLYTKT QDPAKAPNTP DILEIEFKKG VPVKVTNVKD
GTTHQTSLEL FMYLNEVAGK HGVGRIDIVE NRFIGMKSRG IYETPAGTIL YHAHLDIEAF
TMDREVRKIK QGLGLKFAEL VYTGFWHSPE CEFVRHCIAK SQERVEGKVQ VSVLKGQVYI
LGRESPLSLY NEELVSMNVQ GDYEPTDATG FININSLRLK EYHRLQSKVT AK*

speed

0.12 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998782306832 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM146379)
known disease mutation at this position (HGMD CM900033)
known disease mutation: rs6326 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133346264G>AN/A show variant in all transcripts IGV

HGNC symbol

ASS1

Ensembl transcript ID

ENST00000334909

Genbank transcript ID

NM_000050

UniProt peptide

P00966

alteration type

single base exchange

alteration region

CDS

DNA changes

c.539G>A
cDNA.895G>A
g.26171G>A

AA changes

S180N Score: 46 explain score(s)

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

180

frameshift

known variant

Reference ID: rs121908638

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.375	1
	2.579	1
(flanking)	0.654	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 marginally increased	26175	wt: 0.9549 / mu: 0.9812 (marginal change - not scored)	wt: AGCATGGATGAGAAC mu: AACATGGATGAGAAC	CATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

180

mutated

all conserved

180

Ptroglodytes

all identical

ENSPTRG00000021473

180

Mmulatta

all identical

ENSMMUG00000019199

180

Fcatus

not conserved

ENSFCAG00000005111

180

Mmusculus

all identical

ENSMUSG00000046687

180

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

179

Drerio

all identical

ENSDARG00000032564

Dmelanogaster

all identical

FBgn0026565

179

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

181

protein features

start (aa)	end (aa)	feature	details
180	180	BINDING	Citrulline.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1595 / 1595

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

357 / 357

chromosome

strand

last intron/exon boundary

1550

theoretical NMD boundary in CDS

1143

length of CDS

1239

coding sequence (CDS) position

539

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

895

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

26171

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

133346264

original gDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered gDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

original cDNA sequence snippet

CACTCCCAAGAACCCGTGGAGCATGGATGAGAACCTCATGC

altered cDNA sequence snippet

CACTCCCAAGAACCCGTGGAACATGGATGAGAACCTCATGC

wildtype AA sequence

mutated AA sequence

MSSKGSVVLA YSGGLDTSCI LVWLKEQGYD VIAYLANIGQ KEDFEEARKK ALKLGAKKVF
IEDVSREFVE EFIWPAIQSS ALYEDRYLLG TSLARPCIAR KQVEIAQREG AKYVSHGATG
KGNDQVRFEL SCYSLAPQIK VIAPWRMPEF YNRFKGRNDL MEYAKQHGIP IPVTPKNPWN
MDENLMHISY EAGILENPKN QAPPGLYTKT QDPAKAPNTP DILEIEFKKG VPVKVTNVKD
GTTHQTSLEL FMYLNEVAGK HGVGRIDIVE NRFIGMKSRG IYETPAGTIL YHAHLDIEAF
TMDREVRKIK QGLGLKFAEL VYTGFWHSPE CEFVRHCIAK SQERVEGKVQ VSVLKGQVYI
LGRESPLSLY NEELVSMNVQ GDYEPTDATG FININSLRLK EYHRLQSKVT AK*

speed

0.20 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

Problems