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: ENST00000368087
Querying Taster for transcript #2: ENST00000356962
Querying Taster for transcript #3: ENST00000476845
Querying Taster for transcript #4: ENST00000354577
MT speed 2.8 s - this script 4.358225 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARG1	disease_causing_automatic	5.90950428153432e-12	simple_aae		affected	0	T204S	single base exchange	rs104893942		show file
ARG1	disease_causing_automatic	1.47720585950402e-09	simple_aae		affected	0	T290S	single base exchange	rs104893942		show file
ARG1	disease_causing_automatic	1.47720585950402e-09	simple_aae		affected	0	T298S	single base exchange	rs104893942		show file
MED23	disease_causing_automatic	5.9828700476591e-05	without_aae		affected	0		single base exchange	rs104893942		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 5.90950428153432e-12 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM910048)
known disease mutation: rs2389 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:131904948C>GN/A show variant in all transcripts IGV

HGNC symbol

ARG1

Ensembl transcript ID

ENST00000476845

Genbank transcript ID

N/A

UniProt peptide

P05089

alteration type

single base exchange

alteration region

CDS

DNA changes

c.611C>G
cDNA.668C>G
g.10665C>G

AA changes

T204S Score: 58 explain score(s)

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

204

frameshift

known variant

Reference ID: rs104893942
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2389 (pathogenic for Arginase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.259	0.095
	1.051	0.1
(flanking)	0.187	0.093

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 decreased	10660	wt: 0.90 / mu: 0.77	wt: GAAGAAGTAACTCGA mu: GAAGAAGTAAGTCGA	AGAA\|gtaa
Donor increased	10664	wt: 0.25 / mu: 0.97	wt: AAGTAACTCGAACAG mu: AAGTAAGTCGAACAG	GTAA\|ctcg
Donor increased	10659	wt: 0.72 / mu: 1.00	wt: AGAAGAAGTAACTCG mu: AGAAGAAGTAAGTCG	AAGA\|agta
Donor marginally increased	10657	wt: 0.2407 / mu: 0.2524 (marginal change - not scored)	wt: CCAGAAGAAGTAACT mu: CCAGAAGAAGTAAGT	AGAA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

204

mutated

all conserved

204

Ptroglodytes

not conserved

ENSPTRG00000018600

204

Mmulatta

not conserved

ENSMMUG00000017540

211

Fcatus

all identical

ENSFCAG00000002068

276

Mmusculus

not conserved

ENSMUSG00000019987

204

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000002189

226

Drerio

not conserved

ENSDARG00000071703

224

Dmelanogaster

not conserved

FBgn0023535

235

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
200	206	HELIX		lost
202	202	CONFLICT	E -> K (in Ref. 3; AAL71547).	might get lost (downstream of altered splice site)
208	220	HELIX		might get lost (downstream of altered splice site)
221	223	STRAND		might get lost (downstream of altered splice site)
227	232	STRAND		might get lost (downstream of altered splice site)
230	230	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
232	232	METAL	Manganese 1.	might get lost (downstream of altered splice site)
232	232	METAL	Manganese 2.	might get lost (downstream of altered splice site)
233	235	HELIX		might get lost (downstream of altered splice site)
234	234	METAL	Manganese 2.	might get lost (downstream of altered splice site)
238	240	TURN		might get lost (downstream of altered splice site)
243	246	STRAND		might get lost (downstream of altered splice site)
254	267	HELIX		might get lost (downstream of altered splice site)
270	276	STRAND		might get lost (downstream of altered splice site)
280	282	HELIX		might get lost (downstream of altered splice site)
286	303	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

711 / 711

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

237 / 237

position of stopcodon in wt / mu cDNA

768 / 768

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

58 / 58

chromosome

strand

last intron/exon boundary

664

theoretical NMD boundary in CDS

556

length of CDS

711

coding sequence (CDS) position

611

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

668

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

10665

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

131904948

original gDNA sequence snippet

GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG

altered gDNA sequence snippet

GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG

original cDNA sequence snippet

CTTTTCAATGACTGAAGTAACTCGAACAGTGAACACAGCAG

altered cDNA sequence snippet

CTTTTCAATGACTGAAGTAAGTCGAACAGTGAACACAGCAG

wildtype AA sequence

MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN
DSPFQIVKNP RSVGKASEQL AGKVAEVKKN GRISLVLGGD HSLAIGSISG HARVHPDLGV
IWVDAHTDIN TPLTTTSGNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVTRTVNTA VAITLACFGL AREGNHKPID YLNPPK*

mutated AA sequence

speed

1.00 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: 1.47720585950402e-09 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM910048)
known disease mutation: rs2389 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:131904948C>GN/A show variant in all transcripts IGV

HGNC symbol

ARG1

Ensembl transcript ID

ENST00000368087

Genbank transcript ID

NM_000045

UniProt peptide

P05089

alteration type

single base exchange

alteration region

CDS

DNA changes

c.869C>G
cDNA.1008C>G
g.10665C>G

AA changes

T290S Score: 58 explain score(s)

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

290

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.259	0.095
	1.051	0.1
(flanking)	0.187	0.093

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	10664	wt: 0.25 / mu: 0.97	wt: AAGTAACTCGAACAG mu: AAGTAAGTCGAACAG	GTAA\|ctcg
Donor increased	10659	wt: 0.72 / mu: 1.00	wt: AGAAGAAGTAACTCG mu: AGAAGAAGTAAGTCG	AAGA\|agta
Donor marginally increased	10657	wt: 0.2407 / mu: 0.2524 (marginal change - not scored)	wt: CCAGAAGAAGTAACT mu: CCAGAAGAAGTAAGT	AGAA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

290

mutated

all conserved

290

Ptroglodytes

all identical

ENSPTRG00000018600

290

Mmulatta

all identical

ENSMMUG00000017540

297

Fcatus

all identical

ENSFCAG00000002068

276

Mmusculus

not conserved

ENSMUSG00000019987

290

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000002189

312

Drerio

not conserved

ENSDARG00000071703

310

Dmelanogaster

not conserved

FBgn0023535

319

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
286	303	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

1108 / 1108

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

140 / 140

chromosome

strand

last intron/exon boundary

942

theoretical NMD boundary in CDS

752

length of CDS

969

coding sequence (CDS) position

869

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

1008

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

10665

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

131904948

original gDNA sequence snippet

GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG

altered gDNA sequence snippet

GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG

original cDNA sequence snippet

GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG

altered cDNA sequence snippet

GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG

wildtype AA sequence

mutated AA sequence

speed

1.02 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1.47720585950402e-09 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM910048)
known disease mutation: rs2389 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:131904948C>GN/A show variant in all transcripts IGV

HGNC symbol

ARG1

Ensembl transcript ID

ENST00000356962

Genbank transcript ID

NM_001244438

UniProt peptide

P05089

alteration type

single base exchange

alteration region

CDS

DNA changes

c.893C>G
cDNA.951C>G
g.10665C>G

AA changes

T298S Score: 58 explain score(s)

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

298

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.259	0.095
	1.051	0.1
(flanking)	0.187	0.093

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	10664	wt: 0.25 / mu: 0.97	wt: AAGTAACTCGAACAG mu: AAGTAAGTCGAACAG	GTAA\|ctcg
Donor increased	10659	wt: 0.72 / mu: 1.00	wt: AGAAGAAGTAACTCG mu: AGAAGAAGTAAGTCG	AAGA\|agta
Donor marginally increased	10657	wt: 0.2407 / mu: 0.2524 (marginal change - not scored)	wt: CCAGAAGAAGTAACT mu: CCAGAAGAAGTAAGT	AGAA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

298

mutated

all conserved

298

Ptroglodytes

all identical

ENSPTRG00000018600

290

Mmulatta

all identical

ENSMMUG00000017540

297

Fcatus

all identical

ENSFCAG00000002068

276

Mmusculus

not conserved

ENSMUSG00000019987

290

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000002189

312

Drerio

not conserved

ENSDARG00000071703

310

Dmelanogaster

not conserved

FBgn0023535

318

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
286	303	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

position of stopcodon in wt / mu cDNA

1051 / 1051

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

59 / 59

chromosome

strand

last intron/exon boundary

885

theoretical NMD boundary in CDS

776

length of CDS

993

coding sequence (CDS) position

893

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

951

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

10665

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

131904948

original gDNA sequence snippet

GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG

altered gDNA sequence snippet

GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG

original cDNA sequence snippet

GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG

altered cDNA sequence snippet

GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG

wildtype AA sequence

MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQVTQNFLI LECDVKDYGD
LPFADIPNDS PFQIVKNPRS VGKASEQLAG KVAEVKKNGR ISLVLGGDHS LAIGSISGHA
RVHPDLGVIW VDAHTDINTP LTTTSGNLHG QPVSFLLKEL KGKIPDVPGF SWVTPCISAK
DIVYIGLRDV DPGEHYILKT LGIKYFSMTE VDRLGIGKVM EETLSYLLGR KKRPIHLSFD
VDGLDPSFTP ATGTPVVGGL TYREGLYITE EIYKTGLLSG LDIMEVNPSL GKTPEEVTRT
VNTAVAITLA CFGLAREGNH KPIDYLNPPK *

mutated AA sequence

speed

0.48 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 5.9828700476591e-05 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM910048)
known disease mutation: rs2389 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:131904948C>GN/A show variant in all transcripts IGV

HGNC symbol

MED23

Ensembl transcript ID

ENST00000354577

Genbank transcript ID

NM_001270521

UniProt peptide

Q9ULK4

alteration type

single base exchange

alteration region

intron

DNA changes

g.44422G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.259	0.095
	1.051	0.1
(flanking)	0.187	0.093

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	44433	wt: 0.9641 / mu: 0.9857 (marginal change - not scored)	wt: ACTGTTCGAGTTACTTCTTCTGGTGTCTTCCCCAGGGATGG mu: ACTGTTCGACTTACTTCTTCTGGTGTCTTCCCCAGGGATGG	ttct\|GGTG
Acc marginally increased	44420	wt: 0.2801 / mu: 0.3174 (marginal change - not scored)	wt: AACTGCTGTGTTCACTGTTCGAGTTACTTCTTCTGGTGTCT mu: AACTGCTGTGTTCACTGTTCGACTTACTTCTTCTGGTGTCT	ttcg\|AGTT
Acc marginally increased	44419	wt: 0.4924 / mu: 0.5412 (marginal change - not scored)	wt: CAACTGCTGTGTTCACTGTTCGAGTTACTTCTTCTGGTGTC mu: CAACTGCTGTGTTCACTGTTCGACTTACTTCTTCTGGTGTC	gttc\|GAGT
Acc increased	44416	wt: 0.22 / mu: 0.25	wt: TTGCAACTGCTGTGTTCACTGTTCGAGTTACTTCTTCTGGT mu: TTGCAACTGCTGTGTTCACTGTTCGACTTACTTCTTCTGGT	actg\|TTCG
Acc gained	44426	0.68	mu: TGTGTTCACTGTTCGACTTACTTCTTCTGGTGTCTTCCCCA	ttac\|TTCT
Acc gained	44432	0.38	mu: CACTGTTCGACTTACTTCTTCTGGTGTCTTCCCCAGGGATG	cttc\|TGGT
Acc gained	44431	0.51	mu: TCACTGTTCGACTTACTTCTTCTGGTGTCTTCCCCAGGGAT	tctt\|CTGG
Acc gained	44429	0.50	mu: GTTCACTGTTCGACTTACTTCTTCTGGTGTCTTCCCCAGGG	cttc\|TTCT

distance from splice site

3901

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

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

157 / 157

chromosome

strand

-1

last intron/exon boundary

4252

theoretical NMD boundary in CDS

4045

length of CDS

4098

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)

44422

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

131904948

original gDNA sequence snippet

CTGCTGTGTTCACTGTTCGAGTTACTTCTTCTGGTGTCTTC

altered gDNA sequence snippet

CTGCTGTGTTCACTGTTCGACTTACTTCTTCTGGTGTCTTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

METQLQSIFE EVVKTEVIEE AFPGMFMDTP EDEKTKLISC LGAFRQFWGG LSQESHEQCI
QWIVKFIHGQ HSPKRISFLY DCLAMAVETG LLPPRLVCES LINSDTLEWE RTQLWALTFK
LVRKIIGGVD YKGVRDLLKV ILEKILTIPN TVSSAVVQQL LAAREVIAYI LERNACLLPA
YFAVTEIRKL YPEGKLPHWL LGNLVSDFVD TFRPTARINS ICGRCSLLPV VNNSGAICNS
WKLDPATLRF PLKGLLPYDK DLFEPQTALL RYVLEQPYSR DMVCNMLGLN KQTLNIAQHK
QRCPVLEDQL VDLVVYAMER SETEEKFDDG GTSQLLWQHL SSQLIFFVLF QFASFPHMVL
SLHQKLAGRG LIKGRDHLMW VLLQFISGSI QKNALADFLP VMKLFDLLYP EKEYIPVPDI
NKPQSTHAFA MTCIWIHLNR KAQNDNSKLQ IPIPHSLRLH HEFLQQSLRN KSLQMNDYKI
ALLCNAYSTN SECFTLPMGA LVETIYGNGI MRIPLPGTNC MASGSITPLP MNLLDSLTVH
AKMSLIHSIA TRVIKLAHAK SSVALAPALV ETYSRLLVYM EIESLGIKGF ISQLLPTVFK
SHAWGILHTL LEMFSYRMHH IQPHYRVQLL SHLHTLAAVA QTNQNQLHLC VESTALRLIT
ALGSSEVQPQ FTRFLSDPKT VLSAESEELN RALILTLARA THVTDFFTGS DSIQGTWCKD
ILQTIMSFTP HNWASHTLSC FPGPLQAFFK QNNVPQESRF NLKKNVEEEY RKWKSMSNEN
DIITHFSMQG SPPLFLCLLW KMLLETDHIN QIGYRVLERI GARALVAHVR TFADFLVYEF
STSAGGQQLN KCIEILNDMV WKYNIVTLDR LILCLAMRSH EGNEAQVCYF IIQLLLLKPN
DFRNRVSDFV KENSPEHWLQ NDWHTKHMNY HKKYPEKLYF EGLAEQVDPP VQIQSPYLPI
YFGNVCLRFL PVFDIVIHRF LELLPVSKSL ETLLDHLGGL YKFHDRPVTY LYNTLHYYEM
HLRDRAFLKR KLVHAIIGSL KDNRPQGWCL SDTYLKCAMN AREENPWVPD DTYYCRLIGR
LVDTMAGKSP GPFPNCDWRF NEFPNPAAHA LHVTCVELMA LAVSGKEVGN ALLNVVLKSQ
PLVPRENITA WMNAIGLIIT ALPEPYWIVL HDRIVSVISS PSLTSETEWV GYPFRLFDFT
ACHQSYSEMS CSYTLALAHA VWHHSSIGQL SLIPKFLTEV LLPIVKTEFQ LLYVYHLVGP
FLQRFQQERT RCMIEIGVAF YDMLLNVDQC STHLNYMDPI CDFLYHMKYM FTGDSVKEQV
EKIICNLKPA LKLRLRFITH ISKMEPAAVP PQAMNSGSPA PQSNQ*

mutated AA sequence

N/A

speed

0.30 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