MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000354484
Querying Taster for transcript #2: ENST00000393061
Querying Taster for transcript #3: ENST00000393060
MT speed 0 s - this script 4.810852 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADAMTSL2	disease_causing_automatic	0.999999999097681	simple_aae			0	P147L	single base exchange	rs113994121		show file
ADAMTSL2	disease_causing_automatic	0.999999999097681	simple_aae			0	P256L	single base exchange	rs113994121		show file
ADAMTSL2	disease_causing_automatic	0.999999999097681	simple_aae			0	P147L	single base exchange	rs113994121		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999097681 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM083474)
known disease mutation: rs693 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:136405747C>TN/A show variant in all transcripts IGV

HGNC symbol

ADAMTSL2

Ensembl transcript ID

ENST00000354484

Genbank transcript ID

NM_001145320

UniProt peptide

Q86TH1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.997C>T
g.8462C>T

AA changes

P147L Score: 98 explain score(s)

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

147

frameshift

known variant

Reference ID: rs113994121

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

known disease mutation: rs693 (pathogenic for Geleophysic dysplasia 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083474)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
SP1, Transcription Factor, SP1 Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.208	1
	5.208	1
(flanking)	-0.966	0.441

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	8455	wt: 0.4314 / mu: 0.4619 (marginal change - not scored)	wt: ATGACTATGTCCACATCTCCAGCAAACCGTGTGACCTGCAC mu: ATGACTATGTCCACATCTCCAGCAAACTGTGTGACCTGCAC	tcca\|GCAA
Donor marginally increased	8455	wt: 0.9950 / mu: 0.9971 (marginal change - not scored)	wt: TCTCCAGCAAACCGT mu: TCTCCAGCAAACTGT	TCCA\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

all identical

ENSPTRG00000022572

256

Mmulatta

all identical

ENSMMUG00000017203

147

Fcatus

all identical

ENSFCAG00000019127

195

Mmusculus

all identical

ENSMUSG00000036040

147

Ggallus

all identical

ENSGALG00000002955

158

Trubripes

all identical

ENSTRUG00000009723

114

Drerio

no alignment

ENSDARG00000074033

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T19D2.1

n/a

Xtropicalis

no alignment

ENSXETG00000023116

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2856 / 2856

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

952 / 952

position of stopcodon in wt / mu cDNA

3413 / 3413

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

558 / 558

chromosome

strand

last intron/exon boundary

3295

theoretical NMD boundary in CDS

2687

length of CDS

2856

coding sequence (CDS) position

440

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

997

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

8462

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

136405747

original gDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered gDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

original cDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered cDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

wildtype AA sequence

MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFREEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKPCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*

mutated AA sequence

MDGRWQCSCW AWFLLVLAVV AGDTVSTGST DNSPTSNSLE GGTDATAFWW GEWTKWTACS
RSCGGGVTSQ ERHCLQQRRK SVPGPGNRTC TGTSKRYQLC RVQECPPDGR SFREEQCVSF
NSHVYNGRTH QWKPLYPDDY VHISSKLCDL HCTTVDGQRQ LMVPARDGTS CKLTDLRGVC
VSGKCEPIGC DGVLFSTHTL DKCGICQGDG SSCTHVTGNY RKGNAHLGYS LVTHIPAGAR
DIQIVERKKS ADVLALADEA GYYFFNGNYK VDSPKNFNIA GTVVKYRRPM DVYETGIEYI
VAQGPTNQGL NVMVWNQNGK SPSITFEYTL LQPPHESRPQ PIYYGFSESA ESQGLDGAGL
MGFVPHNGSL YGQASSERLG LDNRLFGHPG LDMELGPSQG QETNEVCEQA GGGACEGPPR
GKGFRDRNVT GTPLTGDKDD EEVDTHFASQ EFFSANAISD QLLGAGSDLK DFTLNETVNS
IFAQGAPRSS LAESFFVDYE ENEGAGPYLL NGSYLELSSD RVANSSSEAP FPNVSTSLLT
SAGNRTHKAR TRPKARKQGV SPADMYRWKL SSHEPCSATC TTGVMSAYAM CVRYDGVEVD
DSYCDALTRP EPVHEFCAGR ECQPRWETSS WSECSRTCGE GYQFRVVRCW KMLSPGFDSS
VYSDLCEAAE AVRPEERKTC RNPACGPQWE MSEWSECTAK CGERSVVTRD IRCSEDEKLC
DPNTRPVGEK NCTGPPCDRQ WTVSDWGPCS GSCGQGRTIR HVYCKTSDGR VVPESQCQME
TKPLAIHPCG DKNCPAHWLA QDWERCNTTC GRGVKKRLVL CMELANGKPQ TRSGPECGLA
KKPPEESTCF ERPCFKWYTS PWSECTKTCG VGVRMRDVKC YQGTDIVRGC DPLVKPVGRQ
ACDLQPCPTE PPDDSCQDQP GTNCALAIKV NLCGHWYYSK ACCRSCRPPH S*

speed

1.22 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: 0.999999999097681 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM083474)
known disease mutation: rs693 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:136405747C>TN/A show variant in all transcripts IGV

HGNC symbol

ADAMTSL2

Ensembl transcript ID

ENST00000393061

Genbank transcript ID

NM_014694

UniProt peptide

Q86TH1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.767C>T
cDNA.1199C>T
g.8462C>T

AA changes

P256L Score: 98 explain score(s)

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

256

frameshift

known variant

Reference ID: rs113994121

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.208	1
	5.208	1
(flanking)	-0.966	0.441

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	8455	wt: 0.4314 / mu: 0.4619 (marginal change - not scored)	wt: ATGACTATGTCCACATCTCCAGCAAACCGTGTGACCTGCAC mu: ATGACTATGTCCACATCTCCAGCAAACTGTGTGACCTGCAC	tcca\|GCAA
Donor marginally increased	8455	wt: 0.9950 / mu: 0.9971 (marginal change - not scored)	wt: TCTCCAGCAAACCGT mu: TCTCCAGCAAACTGT	TCCA\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

256

mutated

not conserved

256

Ptroglodytes

all identical

ENSPTRG00000022572

256

Mmulatta

all identical

ENSMMUG00000017203

147

Fcatus

all identical

ENSFCAG00000019127

195

Mmusculus

all identical

ENSMUSG00000036040

147

Ggallus

all identical

ENSGALG00000002955

158

Trubripes

all identical

ENSTRUG00000009723

114

Drerio

no alignment

ENSDARG00000074033

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T19D2.1

n/a

Xtropicalis

no alignment

ENSXETG00000023116

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3183 / 3183

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

1061 / 1061

position of stopcodon in wt / mu cDNA

3615 / 3615

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

433 / 433

chromosome

strand

last intron/exon boundary

3497

theoretical NMD boundary in CDS

3014

length of CDS

3183

coding sequence (CDS) position

767

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

1199

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

8462

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

136405747

original gDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered gDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

original cDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered cDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

wildtype AA sequence

MLFEVGEGGG AGEEGKGRGR PGRSLCTHAA PARTAHLAPS ALRSARPFLW EDNLLTRSQG
LPDNHDQLVP DNLEAWALAG PRGLFPKRTL VIWKRIGAGL VVTVALLPRM DGRWQCSCWA
WFLLVLAVVA GDTVSTGSTD NSPTSNSLEG GTDATAFWWG EWTKWTACSR SCGGGVTSQE
RHCLQQRRKS VPGPGNRTCT GTSKRYQLCR VQECPPDGRS FREEQCVSFN SHVYNGRTHQ
WKPLYPDDYV HISSKPCDLH CTTVDGQRQL MVPARDGTSC KLTDLRGVCV SGKCEPIGCD
GVLFSTHTLD KCGICQGDGS SCTHVTGNYR KGNAHLGYSL VTHIPAGARD IQIVERKKSA
DVLALADEAG YYFFNGNYKV DSPKNFNIAG TVVKYRRPMD VYETGIEYIV AQGPTNQGLN
VMVWNQNGKS PSITFEYTLL QPPHESRPQP IYYGFSESAE SQGLDGAGLM GFVPHNGSLY
GQASSERLGL DNRLFGHPGL DMELGPSQGQ ETNEVCEQAG GGACEGPPRG KGFRDRNVTG
TPLTGDKDDE EVDTHFASQE FFSANAISDQ LLGAGSDLKD FTLNETVNSI FAQGAPRSSL
AESFFVDYEE NEGAGPYLLN GSYLELSSDR VANSSSEAPF PNVSTSLLTS AGNRTHKART
RPKARKQGVS PADMYRWKLS SHEPCSATCT TGVMSAYAMC VRYDGVEVDD SYCDALTRPE
PVHEFCAGRE CQPRWETSSW SECSRTCGEG YQFRVVRCWK MLSPGFDSSV YSDLCEAAEA
VRPEERKTCR NPACGPQWEM SEWSECTAKC GERSVVTRDI RCSEDEKLCD PNTRPVGEKN
CTGPPCDRQW TVSDWGPCSG SCGQGRTIRH VYCKTSDGRV VPESQCQMET KPLAIHPCGD
KNCPAHWLAQ DWERCNTTCG RGVKKRLVLC MELANGKPQT RSGPECGLAK KPPEESTCFE
RPCFKWYTSP WSECTKTCGV GVRMRDVKCY QGTDIVRGCD PLVKPVGRQA CDLQPCPTEP
PDDSCQDQPG TNCALAIKVN LCGHWYYSKA CCRSCRPPHS *

mutated AA sequence

MLFEVGEGGG AGEEGKGRGR PGRSLCTHAA PARTAHLAPS ALRSARPFLW EDNLLTRSQG
LPDNHDQLVP DNLEAWALAG PRGLFPKRTL VIWKRIGAGL VVTVALLPRM DGRWQCSCWA
WFLLVLAVVA GDTVSTGSTD NSPTSNSLEG GTDATAFWWG EWTKWTACSR SCGGGVTSQE
RHCLQQRRKS VPGPGNRTCT GTSKRYQLCR VQECPPDGRS FREEQCVSFN SHVYNGRTHQ
WKPLYPDDYV HISSKLCDLH CTTVDGQRQL MVPARDGTSC KLTDLRGVCV SGKCEPIGCD
GVLFSTHTLD KCGICQGDGS SCTHVTGNYR KGNAHLGYSL VTHIPAGARD IQIVERKKSA
DVLALADEAG YYFFNGNYKV DSPKNFNIAG TVVKYRRPMD VYETGIEYIV AQGPTNQGLN
VMVWNQNGKS PSITFEYTLL QPPHESRPQP IYYGFSESAE SQGLDGAGLM GFVPHNGSLY
GQASSERLGL DNRLFGHPGL DMELGPSQGQ ETNEVCEQAG GGACEGPPRG KGFRDRNVTG
TPLTGDKDDE EVDTHFASQE FFSANAISDQ LLGAGSDLKD FTLNETVNSI FAQGAPRSSL
AESFFVDYEE NEGAGPYLLN GSYLELSSDR VANSSSEAPF PNVSTSLLTS AGNRTHKART
RPKARKQGVS PADMYRWKLS SHEPCSATCT TGVMSAYAMC VRYDGVEVDD SYCDALTRPE
PVHEFCAGRE CQPRWETSSW SECSRTCGEG YQFRVVRCWK MLSPGFDSSV YSDLCEAAEA
VRPEERKTCR NPACGPQWEM SEWSECTAKC GERSVVTRDI RCSEDEKLCD PNTRPVGEKN
CTGPPCDRQW TVSDWGPCSG SCGQGRTIRH VYCKTSDGRV VPESQCQMET KPLAIHPCGD
KNCPAHWLAQ DWERCNTTCG RGVKKRLVLC MELANGKPQT RSGPECGLAK KPPEESTCFE
RPCFKWYTSP WSECTKTCGV GVRMRDVKCY QGTDIVRGCD PLVKPVGRQA CDLQPCPTEP
PDDSCQDQPG TNCALAIKVN LCGHWYYSKA CCRSCRPPHS *

speed

1.28 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999097681 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM083474)
known disease mutation: rs693 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:136405747C>TN/A show variant in all transcripts IGV

HGNC symbol

ADAMTSL2

Ensembl transcript ID

ENST00000393060

Genbank transcript ID

N/A

UniProt peptide

Q86TH1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.655C>T
g.8462C>T

AA changes

P147L Score: 98 explain score(s)

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

147

frameshift

known variant

Reference ID: rs113994121

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.208	1
	5.208	1
(flanking)	-0.966	0.441

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	8455	wt: 0.4314 / mu: 0.4619 (marginal change - not scored)	wt: ATGACTATGTCCACATCTCCAGCAAACCGTGTGACCTGCAC mu: ATGACTATGTCCACATCTCCAGCAAACTGTGTGACCTGCAC	tcca\|GCAA
Donor marginally increased	8455	wt: 0.9950 / mu: 0.9971 (marginal change - not scored)	wt: TCTCCAGCAAACCGT mu: TCTCCAGCAAACTGT	TCCA\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

all identical

ENSPTRG00000022572

256

Mmulatta

all identical

ENSMMUG00000017203

147

Fcatus

all identical

ENSFCAG00000019127

195

Mmusculus

all identical

ENSMUSG00000036040

147

Ggallus

all identical

ENSGALG00000002955

158

Trubripes

all identical

ENSTRUG00000009723

114

Drerio

no alignment

ENSDARG00000074033

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T19D2.1

n/a

Xtropicalis

no alignment

ENSXETG00000023116

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2856 / 2856

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

952 / 952

position of stopcodon in wt / mu cDNA

3071 / 3071

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

216 / 216

chromosome

strand

last intron/exon boundary

2953

theoretical NMD boundary in CDS

2687

length of CDS

2856

coding sequence (CDS) position

440

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

655

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

8462

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

136405747

original gDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered gDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

original cDNA sequence snippet

TGTCCACATCTCCAGCAAACCGTGTGACCTGCACTGTACCA

altered cDNA sequence snippet

TGTCCACATCTCCAGCAAACTGTGTGACCTGCACTGTACCA

wildtype AA sequence

mutated AA sequence

speed

1.38 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