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: ENST00000348367
Querying Taster for transcript #2: ENST00000369425
Querying Taster for transcript #3: ENST00000423155
MT speed 0 s - this script 4.910081 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GPAM	polymorphism_automatic	0.999988512310742	simple_aae				E131G	single base exchange	rs10787428		show file
GPAM	polymorphism_automatic	0.999988512310742	simple_aae				E131G	single base exchange	rs10787428		show file
GPAM	polymorphism_automatic	0.999988512310742	simple_aae				E131G	single base exchange	rs10787428		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.14876892575006e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM067418)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:113935379T>CN/A show variant in all transcripts IGV

HGNC symbol

GPAM

Ensembl transcript ID

ENST00000369425

Genbank transcript ID

N/A

UniProt peptide

Q9HCL2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.392A>G
cDNA.556A>G
g.39757A>G

AA changes

E131G Score: 98 explain score(s)

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

131

frameshift

known variant

Reference ID: rs10787428

database	homozygous (C/C)	heterozygous	allele carriers
1000G	774	1230	2004
ExAC	19674	-6581	13093

known disease mutation at this position, please check HGMD for details (HGMD ID CM067418)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.095	0.998
	4.326	1
(flanking)	5.229	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
Acc marginally increased	39747	wt: 0.2065 / mu: 0.2477 (marginal change - not scored)	wt: ATAAGGGCATGTTTGCCACCAATGTGACTGAAAATGTGCTG mu: ATAAGGGCATGTTTGCCACCAATGTGACTGGAAATGTGCTG	acca\|ATGT
Donor marginally increased	39756	wt: 0.9287 / mu: 0.9914 (marginal change - not scored)	wt: TGACTGAAAATGTGC mu: TGACTGGAAATGTGC	ACTG\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

131

mutated

not conserved

131

Ptroglodytes

all identical

ENSPTRG00000002943

131

Mmulatta

all identical

ENSMMUG00000007526

131

Fcatus

not conserved

ENSFCAG00000003194

Mmusculus

all identical

ENSMUSG00000024978

131

Ggallus

all identical

ENSGALG00000008795

130

Trubripes

all conserved

ENSTRUG00000011579

132

Drerio

all identical

ENSDARG00000074169

129

Dmelanogaster

no alignment

FBgn0027579

n/a

Celegans

all conserved

F08F3.2

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2133 / 2133

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

711 / 711

position of stopcodon in wt / mu cDNA

2297 / 2297

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

165 / 165

chromosome

strand

-1

last intron/exon boundary

2145

theoretical NMD boundary in CDS

1930

length of CDS

2133

coding sequence (CDS) position

392

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

556

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

39757

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

113935379

original gDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered gDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

original cDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered cDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

wildtype AA sequence

MDESALTLGT IDVSYLPHSS EYSVGRCKHT SEEWGECGFR PTIFRSATLK WKESLMSRKR
PFVGRCCYSC TPQSWDKFFN PSIPSLGLRN VIYINETHTR HRGWLARRLS YVLFIQERDV
HKGMFATNVT ENVLNSSRVQ EAIAEVAAEL NPDGSAQQQS KAVNKVKKKA KRILQEMVAT
VSPAMIRLTG WVLLKLFNSF FWNIQIHKGQ LEMVKAATET NLPLLFLPVH RSHIDYLLLT
FILFCHNIKA PYIASGNNLN IPIFSTLIHK LGGFFIRRRL DETPDGRKDV LYRALLHGHI
VELLRQQQFL EIFLEGTRSR SGKTSCARAG LLSVVVDTLS TNVIPDILII PVGISYDRII
EGHYNGEQLG KPKKNESLWS VARGVIRMLR KNYGCVRVDF AQPFSLKEYL ESQSQKPVSA
LLSLEQALLP AILPSRPSDA ADEGRDTSIN ESRNATDESL RRRLIANLAE HILFTASKSC
AIMSTHIVAC LLLYRHRQGI DLSTLVEDFF VMKEEVLARD FDLGFSGNSE DVVMHAIQLL
GNCVTITHTS RNDEFFITPS TTVPSVFELN FYSNGVLHVF IMEAIIACSL YAVLNKRGLG
GPTSTPPNLI SQEQLVRKAA SLCYLLSNEG TISLPCQTFY QVCHETVGKF IQYGILTVAE
HDDQEDISPS LAEQQWDKKL PEPLSWRSDE EDEDSDFGEE QRDCYLKVLG *

mutated AA sequence

MDESALTLGT IDVSYLPHSS EYSVGRCKHT SEEWGECGFR PTIFRSATLK WKESLMSRKR
PFVGRCCYSC TPQSWDKFFN PSIPSLGLRN VIYINETHTR HRGWLARRLS YVLFIQERDV
HKGMFATNVT GNVLNSSRVQ EAIAEVAAEL NPDGSAQQQS KAVNKVKKKA KRILQEMVAT
VSPAMIRLTG WVLLKLFNSF FWNIQIHKGQ LEMVKAATET NLPLLFLPVH RSHIDYLLLT
FILFCHNIKA PYIASGNNLN IPIFSTLIHK LGGFFIRRRL DETPDGRKDV LYRALLHGHI
VELLRQQQFL EIFLEGTRSR SGKTSCARAG LLSVVVDTLS TNVIPDILII PVGISYDRII
EGHYNGEQLG KPKKNESLWS VARGVIRMLR KNYGCVRVDF AQPFSLKEYL ESQSQKPVSA
LLSLEQALLP AILPSRPSDA ADEGRDTSIN ESRNATDESL RRRLIANLAE HILFTASKSC
AIMSTHIVAC LLLYRHRQGI DLSTLVEDFF VMKEEVLARD FDLGFSGNSE DVVMHAIQLL
GNCVTITHTS RNDEFFITPS TTVPSVFELN FYSNGVLHVF IMEAIIACSL YAVLNKRGLG
GPTSTPPNLI SQEQLVRKAA SLCYLLSNEG TISLPCQTFY QVCHETVGKF IQYGILTVAE
HDDQEDISPS LAEQQWDKKL PEPLSWRSDE EDEDSDFGEE QRDCYLKVLG *

speed

1.50 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: 1.14876892575006e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM067418)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:113935379T>CN/A show variant in all transcripts IGV

HGNC symbol

GPAM

Ensembl transcript ID

ENST00000348367

Genbank transcript ID

NM_001244949

UniProt peptide

Q9HCL2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.392A>G
cDNA.590A>G
g.39757A>G

AA changes

E131G Score: 98 explain score(s)

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

131

frameshift

known variant

Reference ID: rs10787428

database	homozygous (C/C)	heterozygous	allele carriers
1000G	774	1230	2004
ExAC	19674	-6581	13093

known disease mutation at this position, please check HGMD for details (HGMD ID CM067418)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.095	0.998
	4.326	1
(flanking)	5.229	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
Acc marginally increased	39747	wt: 0.2065 / mu: 0.2477 (marginal change - not scored)	wt: ATAAGGGCATGTTTGCCACCAATGTGACTGAAAATGTGCTG mu: ATAAGGGCATGTTTGCCACCAATGTGACTGGAAATGTGCTG	acca\|ATGT
Donor marginally increased	39756	wt: 0.9287 / mu: 0.9914 (marginal change - not scored)	wt: TGACTGAAAATGTGC mu: TGACTGGAAATGTGC	ACTG\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

131

mutated

not conserved

131

Ptroglodytes

all identical

ENSPTRG00000002943

131

Mmulatta

all identical

ENSMMUG00000007526

131

Fcatus

not conserved

ENSFCAG00000003194

Mmusculus

all identical

ENSMUSG00000024978

131

Ggallus

all identical

ENSGALG00000008795

130

Trubripes

all conserved

ENSTRUG00000011579

132

Drerio

all identical

ENSDARG00000074169

129

Dmelanogaster

no alignment

FBgn0027579

n/a

Celegans

all conserved

F08F3.2

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2487 / 2487

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

829 / 829

position of stopcodon in wt / mu cDNA

2685 / 2685

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

199 / 199

chromosome

strand

-1

last intron/exon boundary

2569

theoretical NMD boundary in CDS

2320

length of CDS

2487

coding sequence (CDS) position

392

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

590

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

39757

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

113935379

original gDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered gDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

original cDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered cDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

wildtype AA sequence

mutated AA sequence

speed

1.36 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.14876892575006e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM067418)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:113935379T>CN/A show variant in all transcripts IGV

HGNC symbol

GPAM

Ensembl transcript ID

ENST00000423155

Genbank transcript ID

N/A

UniProt peptide

Q9HCL2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.392A>G
cDNA.590A>G
g.39757A>G

AA changes

E131G Score: 98 explain score(s)

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

131

frameshift

known variant

Reference ID: rs10787428

database	homozygous (C/C)	heterozygous	allele carriers
1000G	774	1230	2004
ExAC	19674	-6581	13093

known disease mutation at this position, please check HGMD for details (HGMD ID CM067418)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.095	0.998
	4.326	1
(flanking)	5.229	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
Acc marginally increased	39747	wt: 0.2065 / mu: 0.2477 (marginal change - not scored)	wt: ATAAGGGCATGTTTGCCACCAATGTGACTGAAAATGTGCTG mu: ATAAGGGCATGTTTGCCACCAATGTGACTGGAAATGTGCTG	acca\|ATGT
Donor marginally increased	39756	wt: 0.9287 / mu: 0.9914 (marginal change - not scored)	wt: TGACTGAAAATGTGC mu: TGACTGGAAATGTGC	ACTG\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

131

mutated

not conserved

131

Ptroglodytes

all identical

ENSPTRG00000002943

131

Mmulatta

all identical

ENSMMUG00000007526

131

Fcatus

not conserved

ENSFCAG00000003194

Mmusculus

all identical

ENSMUSG00000024978

131

Ggallus

all identical

ENSGALG00000008795

130

Trubripes

all conserved

ENSTRUG00000011579

132

Drerio

all identical

ENSDARG00000074169

129

Dmelanogaster

no alignment

FBgn0027579

n/a

Celegans

all conserved

F08F3.2

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2487 / 2487

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

829 / 829

position of stopcodon in wt / mu cDNA

2685 / 2685

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

199 / 199

chromosome

strand

-1

last intron/exon boundary

2569

theoretical NMD boundary in CDS

2320

length of CDS

2487

coding sequence (CDS) position

392

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

590

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

39757

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

113935379

original gDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered gDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

original cDNA sequence snippet

GTTTGCCACCAATGTGACTGAAAATGTGCTGAACAGCAGTA

altered cDNA sequence snippet

GTTTGCCACCAATGTGACTGGAAATGTGCTGAACAGCAGTA

wildtype AA sequence

mutated AA sequence

speed

1.38 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems