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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000216194
Querying Taster for transcript #2: ENST00000342312
Querying Taster for transcript #3: ENST00000454266
MT speed 2.88 s - this script 4.1097 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADSL	disease_causing_automatic	0.999999999989804	simple_aae		affected	0	P100A	single base exchange	rs119450942		show file
ADSL	disease_causing_automatic	0.999999999989804	simple_aae		affected	0	P100A	single base exchange	rs119450942		show file
ADSL	disease_causing_automatic	0.999999999989804	simple_aae		affected	0	P100A	single base exchange	rs119450942		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999989804 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980032)
known disease mutation: rs2463 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40745980C>GN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000342312

Genbank transcript ID

NM_001123378

UniProt peptide

P30566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298C>G
cDNA.325C>G
g.3474C>G

AA changes

P100A Score: 27 explain score(s)

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

100

frameshift

known variant

Reference ID: rs119450942

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

known disease mutation: rs2463 (pathogenic for Adenylosuccinate lyase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980032)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980032)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980032)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.071	0.994
	5.874	1
(flanking)	4.288	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	3473	0.79	mu: TGCTGTGCAAAAGCT	CTGT\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

all identical

ENSPTRG00000014407

100

Mmulatta

no alignment

ENSMMUG00000005341

n/a

Fcatus

all identical

ENSFCAG00000004798

100

Mmusculus

all identical

ENSMUSG00000022407

100

Ggallus

all identical

ENSGALG00000012034

101

Trubripes

all identical

ENSTRUG00000001024

116

Drerio

all identical

ENSDARG00000017049

Dmelanogaster

all identical

FBgn0038467

Celegans

all identical

R06C7.5

Xtropicalis

all identical

ENSXETG00000006328

119

protein features

start (aa)	end (aa)	feature	details
100	102	TURN		lost
103	105	HELIX		might get lost (downstream of altered splice site)
106	109	TURN		might get lost (downstream of altered splice site)
113	148	HELIX		might get lost (downstream of altered splice site)
147	147	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
149	151	TURN		might get lost (downstream of altered splice site)
153	158	STRAND		might get lost (downstream of altered splice site)
159	159	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
161	167	STRAND		might get lost (downstream of altered splice site)
168	192	HELIX		might get lost (downstream of altered splice site)
201	204	STRAND		might get lost (downstream of altered splice site)
206	211	HELIX		might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
216	229	HELIX		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
246	274	HELIX		might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
295	295	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
299	313	HELIX		might get lost (downstream of altered splice site)
316	323	HELIX		might get lost (downstream of altered splice site)
331	333	HELIX		might get lost (downstream of altered splice site)
334	360	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
382	389	HELIX		might get lost (downstream of altered splice site)
396	416	HELIX		might get lost (downstream of altered splice site)
423	429	HELIX		might get lost (downstream of altered splice site)
431	433	HELIX		might get lost (downstream of altered splice site)
434	437	HELIX		might get lost (downstream of altered splice site)
440	443	HELIX		might get lost (downstream of altered splice site)
446	449	HELIX		might get lost (downstream of altered splice site)
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1278 / 1278

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

426 / 426

position of stopcodon in wt / mu cDNA

1305 / 1305

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

28 / 28

chromosome

strand

last intron/exon boundary

1219

theoretical NMD boundary in CDS

1141

length of CDS

1278

coding sequence (CDS) position

298

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

325

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

3474

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

40745980

original gDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered gDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

original cDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered cDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

wildtype AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQVQR FLEEEVYPLL KPYESVMKVK
AELCL*

mutated AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCA KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQVQR FLEEEVYPLL KPYESVMKVK
AELCL*

speed

1.13 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: 0.999999999989804 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980032)
known disease mutation: rs2463 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40745980C>GN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000216194

Genbank transcript ID

NM_000026

UniProt peptide

P30566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298C>G
cDNA.354C>G
g.3474C>G

AA changes

P100A Score: 27 explain score(s)

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

100

frameshift

known variant

Reference ID: rs119450942

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

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.071	0.994
	5.874	1
(flanking)	4.288	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	3473	0.79	mu: TGCTGTGCAAAAGCT	CTGT\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

all identical

ENSPTRG00000014407

100

Mmulatta

no alignment

ENSMMUG00000005341

n/a

Fcatus

all identical

ENSFCAG00000004798

100

Mmusculus

all identical

ENSMUSG00000022407

100

Ggallus

all identical

ENSGALG00000012034

101

Trubripes

all identical

ENSTRUG00000001024

116

Drerio

all identical

ENSDARG00000017049

Dmelanogaster

all identical

FBgn0038467

Celegans

all identical

R06C7.5

Xtropicalis

all identical

ENSXETG00000006328

119

protein features

start (aa)	end (aa)	feature	details
100	102	TURN		lost
103	105	HELIX		might get lost (downstream of altered splice site)
106	109	TURN		might get lost (downstream of altered splice site)
113	148	HELIX		might get lost (downstream of altered splice site)
147	147	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
149	151	TURN		might get lost (downstream of altered splice site)
153	158	STRAND		might get lost (downstream of altered splice site)
159	159	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
161	167	STRAND		might get lost (downstream of altered splice site)
168	192	HELIX		might get lost (downstream of altered splice site)
201	204	STRAND		might get lost (downstream of altered splice site)
206	211	HELIX		might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
216	229	HELIX		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
246	274	HELIX		might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
295	295	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
299	313	HELIX		might get lost (downstream of altered splice site)
316	323	HELIX		might get lost (downstream of altered splice site)
331	333	HELIX		might get lost (downstream of altered splice site)
334	360	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
382	389	HELIX		might get lost (downstream of altered splice site)
396	416	HELIX		might get lost (downstream of altered splice site)
423	429	HELIX		might get lost (downstream of altered splice site)
431	433	HELIX		might get lost (downstream of altered splice site)
434	437	HELIX		might get lost (downstream of altered splice site)
440	443	HELIX		might get lost (downstream of altered splice site)
446	449	HELIX		might get lost (downstream of altered splice site)
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1455 / 1455

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

485 / 485

position of stopcodon in wt / mu cDNA

1511 / 1511

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

57 / 57

chromosome

strand

last intron/exon boundary

1425

theoretical NMD boundary in CDS

1318

length of CDS

1455

coding sequence (CDS) position

298

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

354

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

3474

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

40745980

original gDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered gDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

original cDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered cDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

wildtype AA sequence

mutated AA sequence

speed

0.88 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999989804 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980032)
known disease mutation: rs2463 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40745980C>GN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000454266

Genbank transcript ID

N/A

UniProt peptide

P30566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298C>G
cDNA.329C>G
g.3474C>G

AA changes

P100A Score: 27 explain score(s)

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

100

frameshift

known variant

Reference ID: rs119450942

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

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.071	0.994
	5.874	1
(flanking)	4.288	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	3473	0.79	mu: TGCTGTGCAAAAGCT	CTGT\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

all identical

ENSPTRG00000014407

100

Mmulatta

no alignment

ENSMMUG00000005341

n/a

Fcatus

all identical

ENSFCAG00000004798

100

Mmusculus

all identical

ENSMUSG00000022407

100

Ggallus

all identical

ENSGALG00000012034

101

Trubripes

all identical

ENSTRUG00000001024

116

Drerio

all identical

ENSDARG00000017049

Dmelanogaster

all identical

FBgn0038467

Celegans

all identical

R06C7.5

Xtropicalis

all identical

ENSXETG00000006328

119

protein features

start (aa)	end (aa)	feature	details
100	102	TURN		lost
103	105	HELIX		might get lost (downstream of altered splice site)
106	109	TURN		might get lost (downstream of altered splice site)
113	148	HELIX		might get lost (downstream of altered splice site)
147	147	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
149	151	TURN		might get lost (downstream of altered splice site)
153	158	STRAND		might get lost (downstream of altered splice site)
159	159	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
161	167	STRAND		might get lost (downstream of altered splice site)
168	192	HELIX		might get lost (downstream of altered splice site)
201	204	STRAND		might get lost (downstream of altered splice site)
206	211	HELIX		might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
216	229	HELIX		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
246	274	HELIX		might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
295	295	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
299	313	HELIX		might get lost (downstream of altered splice site)
316	323	HELIX		might get lost (downstream of altered splice site)
331	333	HELIX		might get lost (downstream of altered splice site)
334	360	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
382	389	HELIX		might get lost (downstream of altered splice site)
396	416	HELIX		might get lost (downstream of altered splice site)
423	429	HELIX		might get lost (downstream of altered splice site)
431	433	HELIX		might get lost (downstream of altered splice site)
434	437	HELIX		might get lost (downstream of altered splice site)
440	443	HELIX		might get lost (downstream of altered splice site)
446	449	HELIX		might get lost (downstream of altered splice site)
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

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

499 / 499

position of stopcodon in wt / mu cDNA

1528 / 1528

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

32 / 32

chromosome

strand

last intron/exon boundary

1442

theoretical NMD boundary in CDS

1360

length of CDS

1497

coding sequence (CDS) position

298

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

329

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

3474

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

40745980

original gDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered gDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

original cDNA sequence snippet

ACACATTTGGCCACTGCTGTCCAAAAGCTGCAGGCATTATT

altered cDNA sequence snippet

ACACATTTGGCCACTGCTGTGCAAAAGCTGCAGGCATTATT

wildtype AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTS
LILSRGVIKA YCNLRLPGSD SSPVSVSQLA RVISRLADFA KERASLPTLG FTHFQPAQLT
TVGKRCCLWI QDLCMDLQNL KRVRDDLRFR GVKGTTGTQA SFLQLFEGDD HKVEQLDKMV
TEKAGFKRAF IITGQTYTRK VDIEVLSVLA SLGASVHKIC TDIRLLANLK EMEEPFEKQQ
IGSSAMPYKR NPMRSERCCS LARHLMTLVM DPLQTASVQW FERTLDDSAN RRICLAEAFL
TADTILNTLQ NISEGLVVYP KVIERRIRQE LPFMATENII MAMVKAGGSR QDCHEKIRVL
SQQAASVVKQ EGGDNDLIER IQVDAYFSPI HSQLDHLLDP SSFTGRASQQ VQRFLEEEVY
PLLKPYESVM KVKAELCL*

mutated AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCA KAAGIIHLGA TSCYVGDNTS
LILSRGVIKA YCNLRLPGSD SSPVSVSQLA RVISRLADFA KERASLPTLG FTHFQPAQLT
TVGKRCCLWI QDLCMDLQNL KRVRDDLRFR GVKGTTGTQA SFLQLFEGDD HKVEQLDKMV
TEKAGFKRAF IITGQTYTRK VDIEVLSVLA SLGASVHKIC TDIRLLANLK EMEEPFEKQQ
IGSSAMPYKR NPMRSERCCS LARHLMTLVM DPLQTASVQW FERTLDDSAN RRICLAEAFL
TADTILNTLQ NISEGLVVYP KVIERRIRQE LPFMATENII MAMVKAGGSR QDCHEKIRVL
SQQAASVVKQ EGGDNDLIER IQVDAYFSPI HSQLDHLLDP SSFTGRASQQ VQRFLEEEVY
PLLKPYESVM KVKAELCL*

speed

0.87 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems