MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: 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 6.032682 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ASS1	disease_causing_automatic	0.999999990480569	simple_aae		affected	0	G390R	single base exchange	rs121908641		show file
ASS1	disease_causing_automatic	0.999999990480569	simple_aae		affected	0	G390R	single base exchange	rs121908641		show file
ASS1	disease_causing_automatic	0.999999990480569	simple_aae		affected	0	G390R	single base exchange	rs121908641		show file
ASS1	disease_causing_automatic	0.999999990480569	simple_aae		affected	0	G390R	single base exchange	rs121908641		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999990480569 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM900037)
known disease mutation: rs6329 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133374932G>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.1168G>A
cDNA.1240G>A
g.54839G>A

AA changes

G390R Score: 125 explain score(s)

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

390

frameshift

known variant

Reference ID: rs121908641

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	45	45

known disease mutation: rs6329 (pathogenic for Citrullinemia type I|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900037)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900037)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900037)

regulatory features

H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.641	0.957
	3.796	1
(flanking)	3.796	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 gained	54835	0.73	mu: GATGCCACCAGGTTC	TGCC\|acca
Donor gained	54839	0.32	mu: CCACCAGGTTCATCA	ACCA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

not conserved

390

Ptroglodytes

all identical

ENSPTRG00000021473

390

Mmulatta

all identical

ENSMMUG00000019199

390

Fcatus

no alignment

ENSFCAG00000005111

n/a

Mmusculus

all identical

ENSMUSG00000046687

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

389

Drerio

all identical

ENSDARG00000032564

250

Dmelanogaster

all identical

FBgn0026565

390

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

392

protein features

start (aa)	end (aa)	feature	details
385	404	HELIX		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

1168

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

1240

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

54839

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

133374932

original gDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered gDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

original cDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered cDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

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

speed

1.37 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: 0.999999990480569 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM900037)
known disease mutation: rs6329 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133374932G>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.1168G>A
cDNA.1649G>A
g.54839G>A

AA changes

G390R Score: 125 explain score(s)

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

390

frameshift

known variant

Reference ID: rs121908641

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	45	45

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.641	0.957
	3.796	1
(flanking)	3.796	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 gained	54835	0.73	mu: GATGCCACCAGGTTC	TGCC\|acca
Donor gained	54839	0.32	mu: CCACCAGGTTCATCA	ACCA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

not conserved

390

Ptroglodytes

all identical

ENSPTRG00000021473

390

Mmulatta

all identical

ENSMMUG00000019199

390

Fcatus

no alignment

ENSFCAG00000005111

n/a

Mmusculus

all identical

ENSMUSG00000046687

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

389

Drerio

all identical

ENSDARG00000032564

250

Dmelanogaster

all identical

FBgn0026565

390

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

392

protein features

start (aa)	end (aa)	feature	details
385	404	HELIX		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

1168

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

1649

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

54839

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

133374932

original gDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered gDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

original cDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered cDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

wildtype AA sequence

mutated AA sequence

speed

1.26 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999990480569 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM900037)
known disease mutation: rs6329 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133374932G>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.1168G>A
cDNA.1241G>A
g.54839G>A

AA changes

G390R Score: 125 explain score(s)

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

390

frameshift

known variant

Reference ID: rs121908641

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	45	45

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.641	0.957
	3.796	1
(flanking)	3.796	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 gained	54835	0.73	mu: GATGCCACCAGGTTC	TGCC\|acca
Donor gained	54839	0.32	mu: CCACCAGGTTCATCA	ACCA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

not conserved

390

Ptroglodytes

all identical

ENSPTRG00000021473

390

Mmulatta

all identical

ENSMMUG00000019199

390

Fcatus

no alignment

ENSFCAG00000005111

n/a

Mmusculus

all identical

ENSMUSG00000046687

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

389

Drerio

all identical

ENSDARG00000032564

250

Dmelanogaster

all identical

FBgn0026565

390

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

392

protein features

start (aa)	end (aa)	feature	details
385	404	HELIX		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

1168

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

1241

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

54839

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

133374932

original gDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered gDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

original cDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered cDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

wildtype AA sequence

mutated AA sequence

speed

1.26 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999990480569 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM900037)
known disease mutation: rs6329 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:133374932G>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.1168G>A
cDNA.1524G>A
g.54839G>A

AA changes

G390R Score: 125 explain score(s)

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

390

frameshift

known variant

Reference ID: rs121908641

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	45	45

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.641	0.957
	3.796	1
(flanking)	3.796	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 gained	54835	0.73	mu: GATGCCACCAGGTTC	TGCC\|acca
Donor gained	54839	0.32	mu: CCACCAGGTTCATCA	ACCA\|ggtt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

390

mutated

not conserved

390

Ptroglodytes

all identical

ENSPTRG00000021473

390

Mmulatta

all identical

ENSMMUG00000019199

390

Fcatus

no alignment

ENSFCAG00000005111

n/a

Mmusculus

all identical

ENSMUSG00000046687

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018657

389

Drerio

all identical

ENSDARG00000032564

250

Dmelanogaster

all identical

FBgn0026565

390

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001347

392

protein features

start (aa)	end (aa)	feature	details
385	404	HELIX		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

1168

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

1524

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

54839

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

133374932

original gDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered gDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

original cDNA sequence snippet

ATGAGCCAACTGATGCCACCGGGTTCATCAACATCAATTCC

altered cDNA sequence snippet

ATGAGCCAACTGATGCCACCAGGTTCATCAACATCAATTCC

wildtype AA sequence

mutated AA sequence

speed

1.36 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