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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000299698
Querying Taster for transcript #2: ENST00000539547
MT speed 0 s - this script 6.416318 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
A2ML1	polymorphism_automatic	1.41072300507972e-08	simple_aae				R631W	single base exchange	rs1860967		show file
A2ML1	polymorphism_automatic	1.41072300507972e-08	simple_aae				R1122W	single base exchange	rs1860967		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999998589277 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:9013755C>TN/A show variant in all transcripts IGV

HGNC symbol

A2ML1

Ensembl transcript ID

ENST00000539547

Genbank transcript ID

N/A

UniProt peptide

A8K2U0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1891C>T
cDNA.2059C>T
g.38688C>T

AA changes

R631W Score: 101 explain score(s)

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

631

frameshift

known variant

Reference ID: rs1860967

database	homozygous (T/T)	heterozygous	allele carriers
1000G	623	919	1542
ExAC	12818	7131	19949

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.989	0.427
	-0.145	0.282
(flanking)	0.212	0.285

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	38693	wt: 0.7760 / mu: 0.8182 (marginal change - not scored)	wt: CGGTGTCTCAAGAAT mu: TGGTGTCTCAAGAAT	GTGT\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

631

mutated

not conserved

631

Ptroglodytes

all identical

ENSPTRG00000004645

1122

Mmulatta

all conserved

ENSMMUG00000022680

1120

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000019254

603

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

not conserved

ZK337.1

1144

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2892 / 2892

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

964 / 964

position of stopcodon in wt / mu cDNA

3060 / 3060

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

169 / 169

chromosome

strand

last intron/exon boundary

3062

theoretical NMD boundary in CDS

2843

length of CDS

2892

coding sequence (CDS) position

1891

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

2059

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

38688

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

9013755

original gDNA sequence snippet

CAATGGTGAGTCAGGGTCTACGGTGTCTCAAGAATTCGGCC

altered gDNA sequence snippet

CAATGGTGAGTCAGGGTCTATGGTGTCTCAAGAATTCGGCC

original cDNA sequence snippet

CAATGGTGAGTCAGGGTCTACGGTGTCTCAAGAATTCGGCC

altered cDNA sequence snippet

CAATGGTGAGTCAGGGTCTATGGTGTCTCAAGAATTCGGCC

wildtype AA sequence

MLIGKGSLVM EGQKHLNSKK KGLKASFSLS LTFTSRLAPD PSLVIYAIFP SGGVVADKIQ
FSVEMCFDNQ VSLGFSPSQQ LPGAEVELQL QAAPGSLCAL RAVDESVLLL RPDRELSNRS
VYGMFPFWYG HYPYQVAEYD QCPVSGPWDF PQPLIDPMPQ GHSSQRSIIW RPSFSEGTDL
FSFFRDVGLK ILSNAKIKKP VDCSHRSPEY STAMGAGGGH PEAFESSTPL HQAEDSQVRQ
YFPETWLWDL FPIGNSGKEA VHVTVPDAIT EWKAMSFCTS QSRGFGLSPT VGLTAFKPFF
VDLTLPYSVV RGESFRLTAT IFNYLKDCIR VQTDLAKSHE YQLESWADSQ TSSCLCADDA
KTHHWNITAV KLGHINFTIS TKILDSNEPC GGQKGFVPQK GRSDTLIKPV LVKPEGVLVE
KTHSSLLCPK GKVASESVSL ELPVDIVPDS TKAYVTVLGD IMGTALQNLD GLVQMPSGCG
EQNMVLFAPI IYVLQYLEKA GLLTEEIRSR AVGFLEIGYQ KELMYKHSNG SYSAFGERDG
NGNTWLTAFV TKCFGQAQKF IFIDPKNIQD ALKWMAGNQL PSGCYANVGN LLHTAMKGGV
DDEVSLTAYV TAALLEMGKD VDDPMVSQGL RCLKNSATST TNLYTQALLA YIFSLAGEMD
IRNILLKQLD QQAIISGESI YWSQKPTPSS NASPWSEPAA VDVELTAYAL LAQLTKPSLT
QKEIAKATSI VAWLAKQHNA YGGFSSTQDT VVALQALAKY ATTAYMPSEE INLVVKSTEN
FQRTFNIQSV NRLVFQQDTL PNVPGMYTLE ASGQGCVYVQ TVLRYNILPP TNMKTFSLSV
EIGKARCEQP TSPRSLTLTI HTSYVGSRSS SNMAIVEVKM LSGFSPMEGT NQLLLQQPLV
KKVEFGTDTL NIYLDELIKN TQTYTFTISQ SVLVTNLKPA TIKVYDYYLP DEQATIQYSD
PCE*

mutated AA sequence

MLIGKGSLVM EGQKHLNSKK KGLKASFSLS LTFTSRLAPD PSLVIYAIFP SGGVVADKIQ
FSVEMCFDNQ VSLGFSPSQQ LPGAEVELQL QAAPGSLCAL RAVDESVLLL RPDRELSNRS
VYGMFPFWYG HYPYQVAEYD QCPVSGPWDF PQPLIDPMPQ GHSSQRSIIW RPSFSEGTDL
FSFFRDVGLK ILSNAKIKKP VDCSHRSPEY STAMGAGGGH PEAFESSTPL HQAEDSQVRQ
YFPETWLWDL FPIGNSGKEA VHVTVPDAIT EWKAMSFCTS QSRGFGLSPT VGLTAFKPFF
VDLTLPYSVV RGESFRLTAT IFNYLKDCIR VQTDLAKSHE YQLESWADSQ TSSCLCADDA
KTHHWNITAV KLGHINFTIS TKILDSNEPC GGQKGFVPQK GRSDTLIKPV LVKPEGVLVE
KTHSSLLCPK GKVASESVSL ELPVDIVPDS TKAYVTVLGD IMGTALQNLD GLVQMPSGCG
EQNMVLFAPI IYVLQYLEKA GLLTEEIRSR AVGFLEIGYQ KELMYKHSNG SYSAFGERDG
NGNTWLTAFV TKCFGQAQKF IFIDPKNIQD ALKWMAGNQL PSGCYANVGN LLHTAMKGGV
DDEVSLTAYV TAALLEMGKD VDDPMVSQGL WCLKNSATST TNLYTQALLA YIFSLAGEMD
IRNILLKQLD QQAIISGESI YWSQKPTPSS NASPWSEPAA VDVELTAYAL LAQLTKPSLT
QKEIAKATSI VAWLAKQHNA YGGFSSTQDT VVALQALAKY ATTAYMPSEE INLVVKSTEN
FQRTFNIQSV NRLVFQQDTL PNVPGMYTLE ASGQGCVYVQ TVLRYNILPP TNMKTFSLSV
EIGKARCEQP TSPRSLTLTI HTSYVGSRSS SNMAIVEVKM LSGFSPMEGT NQLLLQQPLV
KKVEFGTDTL NIYLDELIKN TQTYTFTISQ SVLVTNLKPA TIKVYDYYLP DEQATIQYSD
PCE*

speed

1.89 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

polymorphism

Model: simple_aae, prob: 0.99999998589277 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:9013755C>TN/A show variant in all transcripts IGV

HGNC symbol

A2ML1

Ensembl transcript ID

ENST00000299698

Genbank transcript ID

NM_144670

UniProt peptide

A8K2U0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3364C>T
cDNA.3544C>T
g.38688C>T

AA changes

R1122W Score: 101 explain score(s)

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

1122

frameshift

known variant

Reference ID: rs1860967

database	homozygous (T/T)	heterozygous	allele carriers
1000G	623	919	1542
ExAC	12818	7131	19949

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.989	0.427
	-0.145	0.282
(flanking)	0.212	0.285

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	38693	wt: 0.7760 / mu: 0.8182 (marginal change - not scored)	wt: CGGTGTCTCAAGAAT mu: TGGTGTCTCAAGAAT	GTGT\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1122

mutated

not conserved

1122

Ptroglodytes

all identical

ENSPTRG00000004645

1122

Mmulatta

all conserved

ENSMMUG00000022680

1120

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000019254

603

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

not conserved

ZK337.1

1145

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1122	1122	CONFLICT	R -> W (in Ref. 1; BAC04793/BAC85653/ BAC85654/BAF83044 and 2; AL832139).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4365 / 4365

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

1455 / 1455

position of stopcodon in wt / mu cDNA

4545 / 4545

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

181 / 181

chromosome

strand

last intron/exon boundary

4547

theoretical NMD boundary in CDS

4316

length of CDS

4365

coding sequence (CDS) position

3364

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

3544

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

38688

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

9013755

original gDNA sequence snippet

CAATGGTGAGTCAGGGTCTACGGTGTCTCAAGAATTCGGCC

altered gDNA sequence snippet

CAATGGTGAGTCAGGGTCTATGGTGTCTCAAGAATTCGGCC

original cDNA sequence snippet

CAATGGTGAGTCAGGGTCTACGGTGTCTCAAGAATTCGGCC

altered cDNA sequence snippet

CAATGGTGAGTCAGGGTCTATGGTGTCTCAAGAATTCGGCC

wildtype AA sequence

MWAQLLLGML ALSPAIAEEL PNYLVTLPAR LNFPSVQKVC LDLSPGYSDV KFTVTLETKD
KTQKLLEYSG LKKRHLHCIS FLVPPPAGGT EEVATIRVSG VGNNISFEEK KKVLIQRQGN
GTFVQTDKPL YTPGQQVYFR IVTMDSNFVP VNDKYSMVEL QDPNSNRIAQ WLEVVPEQGI
VDLSFQLAPE AMLGTYTVAV AEGKTFGTFS VEEYVLPKFK VEVVEPKELS TVQESFLVKI
CCRYTYGKPM LGAVQVSVCQ KANTYWYREV EREQLPDKCR NLSGQTDKTG CFSAPVDMAT
FDLIGYAYSH QINIVATVVE EGTGVEANAT QNIYISPQMG SMTFEDTSNF YHPNFPFSGK
IRVRGHDDSF LKNHLVFLVI YGTNGTFNQT LVTDNNGLAP FTLETSGWNG TDVSLEGKFQ
MEDLVYNPEQ VPRYYQNAYL HLRPFYSTTR SFLGIHRLNG PLKCGQPQEV LVDYYIDPAD
ASPDQEISFS YYLIGKGSLV MEGQKHLNSK KKGLKASFSL SLTFTSRLAP DPSLVIYAIF
PSGGVVADKI QFSVEMCFDN QVSLGFSPSQ QLPGAEVELQ LQAAPGSLCA LRAVDESVLL
LRPDRELSNR SVYGMFPFWY GHYPYQVAEY DQCPVSGPWD FPQPLIDPMP QGHSSQRSII
WRPSFSEGTD LFSFFRDVGL KILSNAKIKK PVDCSHRSPE YSTAMGAGGG HPEAFESSTP
LHQAEDSQVR QYFPETWLWD LFPIGNSGKE AVHVTVPDAI TEWKAMSFCT SQSRGFGLSP
TVGLTAFKPF FVDLTLPYSV VRGESFRLTA TIFNYLKDCI RVQTDLAKSH EYQLESWADS
QTSSCLCADD AKTHHWNITA VKLGHINFTI STKILDSNEP CGGQKGFVPQ KGRSDTLIKP
VLVKPEGVLV EKTHSSLLCP KGKVASESVS LELPVDIVPD STKAYVTVLG DIMGTALQNL
DGLVQMPSGC GEQNMVLFAP IIYVLQYLEK AGLLTEEIRS RAVGFLEIGY QKELMYKHSN
GSYSAFGERD GNGNTWLTAF VTKCFGQAQK FIFIDPKNIQ DALKWMAGNQ LPSGCYANVG
NLLHTAMKGG VDDEVSLTAY VTAALLEMGK DVDDPMVSQG LRCLKNSATS TTNLYTQALL
AYIFSLAGEM DIRNILLKQL DQQAIISGES IYWSQKPTPS SNASPWSEPA AVDVELTAYA
LLAQLTKPSL TQKEIAKATS IVAWLAKQHN AYGGFSSTQD TVVALQALAK YATTAYMPSE
EINLVVKSTE NFQRTFNIQS VNRLVFQQDT LPNVPGMYTL EASGQGCVYV QTVLRYNILP
PTNMKTFSLS VEIGKARCEQ PTSPRSLTLT IHTSYVGSRS SSNMAIVEVK MLSGFSPMEG
TNQLLLQQPL VKKVEFGTDT LNIYLDELIK NTQTYTFTIS QSVLVTNLKP ATIKVYDYYL
PDEQATIQYS DPCE*

mutated AA sequence

MWAQLLLGML ALSPAIAEEL PNYLVTLPAR LNFPSVQKVC LDLSPGYSDV KFTVTLETKD
KTQKLLEYSG LKKRHLHCIS FLVPPPAGGT EEVATIRVSG VGNNISFEEK KKVLIQRQGN
GTFVQTDKPL YTPGQQVYFR IVTMDSNFVP VNDKYSMVEL QDPNSNRIAQ WLEVVPEQGI
VDLSFQLAPE AMLGTYTVAV AEGKTFGTFS VEEYVLPKFK VEVVEPKELS TVQESFLVKI
CCRYTYGKPM LGAVQVSVCQ KANTYWYREV EREQLPDKCR NLSGQTDKTG CFSAPVDMAT
FDLIGYAYSH QINIVATVVE EGTGVEANAT QNIYISPQMG SMTFEDTSNF YHPNFPFSGK
IRVRGHDDSF LKNHLVFLVI YGTNGTFNQT LVTDNNGLAP FTLETSGWNG TDVSLEGKFQ
MEDLVYNPEQ VPRYYQNAYL HLRPFYSTTR SFLGIHRLNG PLKCGQPQEV LVDYYIDPAD
ASPDQEISFS YYLIGKGSLV MEGQKHLNSK KKGLKASFSL SLTFTSRLAP DPSLVIYAIF
PSGGVVADKI QFSVEMCFDN QVSLGFSPSQ QLPGAEVELQ LQAAPGSLCA LRAVDESVLL
LRPDRELSNR SVYGMFPFWY GHYPYQVAEY DQCPVSGPWD FPQPLIDPMP QGHSSQRSII
WRPSFSEGTD LFSFFRDVGL KILSNAKIKK PVDCSHRSPE YSTAMGAGGG HPEAFESSTP
LHQAEDSQVR QYFPETWLWD LFPIGNSGKE AVHVTVPDAI TEWKAMSFCT SQSRGFGLSP
TVGLTAFKPF FVDLTLPYSV VRGESFRLTA TIFNYLKDCI RVQTDLAKSH EYQLESWADS
QTSSCLCADD AKTHHWNITA VKLGHINFTI STKILDSNEP CGGQKGFVPQ KGRSDTLIKP
VLVKPEGVLV EKTHSSLLCP KGKVASESVS LELPVDIVPD STKAYVTVLG DIMGTALQNL
DGLVQMPSGC GEQNMVLFAP IIYVLQYLEK AGLLTEEIRS RAVGFLEIGY QKELMYKHSN
GSYSAFGERD GNGNTWLTAF VTKCFGQAQK FIFIDPKNIQ DALKWMAGNQ LPSGCYANVG
NLLHTAMKGG VDDEVSLTAY VTAALLEMGK DVDDPMVSQG LWCLKNSATS TTNLYTQALL
AYIFSLAGEM DIRNILLKQL DQQAIISGES IYWSQKPTPS SNASPWSEPA AVDVELTAYA
LLAQLTKPSL TQKEIAKATS IVAWLAKQHN AYGGFSSTQD TVVALQALAK YATTAYMPSE
EINLVVKSTE NFQRTFNIQS VNRLVFQQDT LPNVPGMYTL EASGQGCVYV QTVLRYNILP
PTNMKTFSLS VEIGKARCEQ PTSPRSLTLT IHTSYVGSRS SSNMAIVEVK MLSGFSPMEG
TNQLLLQQPL VKKVEFGTDT LNIYLDELIK NTQTYTFTIS QSVLVTNLKP ATIKVYDYYL
PDEQATIQYS DPCE*

speed

0.94 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems