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: ENST00000257863
Querying Taster for transcript #2: ENST00000550311
Querying Taster for transcript #3: ENST00000379791
MT speed 0 s - this script 3.496133 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AMHR2	disease_causing_automatic	0.0107045291831511	simple_aae		affected	0	R406Q	single base exchange	rs137853104		show file
AMHR2	disease_causing_automatic	0.0107045291831511	simple_aae		affected	0	R406Q	single base exchange	rs137853104		show file
AMHR2	disease_causing_automatic	0.999999886057409	without_aae		affected	0		single base exchange	rs137853104		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.0107045291831511 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM016199)
known disease mutation: rs8629 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:53823691G>AN/A show variant in all transcripts IGV

HGNC symbol

AMHR2

Ensembl transcript ID

ENST00000257863

Genbank transcript ID

NM_020547

UniProt peptide

Q16671

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1217G>A
cDNA.1297G>A
g.6053G>A

AA changes

R406Q Score: 43 explain score(s)

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

406

frameshift

known variant

Reference ID: rs137853104

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs8629 (pathogenic for Persistent mullerian duct syndrome, type II) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.012	0.989
	0.211	0.985
(flanking)	0.566	0.99

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	6050	wt: 0.39 / mu: 0.47	wt: GGCCCTCCGACGAGC mu: GGCCCTCCAACGAGC	CCCT\|ccga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

406

mutated

all conserved

406

Ptroglodytes

all identical

ENSPTRG00000005015

406

Mmulatta

all identical

ENSMMUG00000020037

406

Fcatus

all identical

ENSFCAG00000005894

411

Mmusculus

all conserved

ENSMUSG00000023047

402

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
171	573	TOPO_DOM	Cytoplasmic (Potential).	lost
203	518	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1722 / 1722

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

574 / 574

position of stopcodon in wt / mu cDNA

1802 / 1802

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

81 / 81

chromosome

strand

last intron/exon boundary

1506

theoretical NMD boundary in CDS

1375

length of CDS

1722

coding sequence (CDS) position

1217

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

1297

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

6053

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

53823691

original gDNA sequence snippet

GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT

altered gDNA sequence snippet

GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT

original cDNA sequence snippet

GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT

altered cDNA sequence snippet

GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT

wildtype AA sequence

MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALRRADI YSLALLLWEI
LSRCPDLRPD SSPPPFQLAY EAELGNTPTS DELWALAVQE RRRPYIPSTW RCFATDPDGL
RELLEDCWDA DPEARLTAEC VQQRLAALAH PQESHPFPES CPRGCPPLCP EDCTSIPAPT
ILPCRPQRSA CHFSVQQGPC SRNPQPACTL SPV*

mutated AA sequence

MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALQRADI YSLALLLWEI
LSRCPDLRPD SSPPPFQLAY EAELGNTPTS DELWALAVQE RRRPYIPSTW RCFATDPDGL
RELLEDCWDA DPEARLTAEC VQQRLAALAH PQESHPFPES CPRGCPPLCP EDCTSIPAPT
ILPCRPQRSA CHFSVQQGPC SRNPQPACTL SPV*

speed

0.87 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: 0.0107045291831511 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM016199)
known disease mutation: rs8629 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:53823691G>AN/A show variant in all transcripts IGV

HGNC symbol

AMHR2

Ensembl transcript ID

ENST00000550311

Genbank transcript ID

NM_001164690

UniProt peptide

Q16671

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1217G>A
cDNA.1286G>A
g.6053G>A

AA changes

R406Q Score: 43 explain score(s)

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

406

frameshift

known variant

Reference ID: rs137853104

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.012	0.989
	0.211	0.985
(flanking)	0.566	0.99

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	6050	wt: 0.39 / mu: 0.47	wt: GGCCCTCCGACGAGC mu: GGCCCTCCAACGAGC	CCCT\|ccga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

406

mutated

all conserved

406

Ptroglodytes

all identical

ENSPTRG00000005015

406

Mmulatta

all identical

ENSMMUG00000020037

406

Fcatus

all identical

ENSFCAG00000005894

411

Mmusculus

all conserved

ENSMUSG00000023047

402

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
171	573	TOPO_DOM	Cytoplasmic (Potential).	lost
203	518	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1437 / 1437

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

479 / 479

position of stopcodon in wt / mu cDNA

1506 / 1506

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

70 / 70

chromosome

strand

last intron/exon boundary

1491

theoretical NMD boundary in CDS

1371

length of CDS

1437

coding sequence (CDS) position

1217

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

1286

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

6053

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

53823691

original gDNA sequence snippet

GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT

altered gDNA sequence snippet

GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT

original cDNA sequence snippet

GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT

altered cDNA sequence snippet

GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT

wildtype AA sequence

MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALRRADI YSLALLLWEI
LSRCPDLRPA VHHPSNWPMR QNWAIPLPLM SYGPWQCRRG GVPTSHPPGA ALPQTLMG*

mutated AA sequence

MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALQRADI YSLALLLWEI
LSRCPDLRPA VHHPSNWPMR QNWAIPLPLM SYGPWQCRRG GVPTSHPPGA ALPQTLMG*

speed

0.68 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 0.999999886057409 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM016199)
known disease mutation: rs8629 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:53823691G>AN/A show variant in all transcripts IGV

HGNC symbol

AMHR2

Ensembl transcript ID

ENST00000379791

Genbank transcript ID

NM_001164691

UniProt peptide

Q16671

alteration type

single base exchange

alteration region

intron

DNA changes

g.6053G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs137853104

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.012	0.989
	0.211	0.985
(flanking)	0.566	0.99

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	6050	wt: 0.39 / mu: 0.47	wt: GGCCCTCCGACGAGC mu: GGCCCTCCAACGAGC	CCCT\|ccga

distance from splice site

282

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
171	573	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
203	518	DOMAIN	Protein kinase.	might get lost (downstream of altered splice site)

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

1 / 1

chromosome

strand

last intron/exon boundary

1141

theoretical NMD boundary in CDS

1090

length of CDS

1437

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)

6053

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

53823691

original gDNA sequence snippet

GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT

altered gDNA sequence snippet

GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME DPDGLRELLE DCWDADPEAR LTAECVQQRL AALAHPQESH
PFPESCPRGC PPLCPEDCTS IPAPTILPCR PQRSACHFSV QQGPCSRNPQ PACTLSPV*

mutated AA sequence

N/A

speed

0.57 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