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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000525682
Querying Taster for transcript #2: ENST00000236342
Querying Taster for transcript #3: ENST00000526219
Querying Taster for transcript #4: ENST00000360009
MT speed 0 s - this script 5.331398 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DHDDS	polymorphism_automatic	7.60946861078082e-13	simple_aae		affected		V253M	single base exchange	rs3816539		show file
DHDDS	polymorphism_automatic	1.77802217393719e-12	simple_aae		affected		V219M	single base exchange	rs3816539		show file
DHDDS	polymorphism_automatic	1.77802217393719e-12	simple_aae		affected		V253M	single base exchange	rs3816539		show file
DHDDS	polymorphism_automatic	1.77802217393719e-12	simple_aae		affected		V214M	single base exchange	rs3816539		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999239 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:26786627G>AN/A show variant in all transcripts IGV

HGNC symbol

DHDDS

Ensembl transcript ID

ENST00000360009

Genbank transcript ID

NM_024887

UniProt peptide

Q86SQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.757G>A
cDNA.834G>A
g.27855G>A

AA changes

V253M Score: 21 explain score(s)

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

253

frameshift

known variant

Reference ID: rs3816539

database	homozygous (A/A)	heterozygous	allele carriers
1000G	574	1132	1706
ExAC	7285	18197	25482

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.335	0.031
	0.028	0.032
(flanking)	0.598	0.1

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
Donor increased	27847	wt: 0.45 / mu: 0.60	wt: GATGAACCATAGCGT mu: GATGAACCATAGCAT	TGAA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

253

mutated

all conserved

253

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022426

253

Fcatus

not conserved

ENSFCAG00000012811

253

Mmusculus

not conserved

ENSMUSG00000012117

253

Ggallus

not conserved

ENSGALG00000000385

253

Trubripes

not conserved

ENSTRUG00000007224

253

Drerio

not conserved

ENSDARG00000039851

253

Dmelanogaster

not conserved

FBgn0029980

253

Celegans

no alignment

T01G1.4

n/a

Xtropicalis

not conserved

ENSXETG00000012322

255

protein features

start (aa)	end (aa)	feature	details
277	277	CONFLICT	V -> E (in Ref. 6; AAH34152).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1005 / 1005

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

335 / 335

position of stopcodon in wt / mu cDNA

1082 / 1082

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

78 / 78

chromosome

strand

last intron/exon boundary

843

theoretical NMD boundary in CDS

715

length of CDS

1005

coding sequence (CDS) position

757

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

834

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

27855

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

26786627

original gDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGGTAAGAAAGAGT

altered gDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGGTAAGAAAGAGT

original cDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGCAGAAGGCCCGA

altered cDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGCAGAAGGCCCGA

wildtype AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNKCFL NVCFAYTSRH EISNAVREMA WGVEQGLLDP
SDISESLLDK CLYTNRSPHP DILIRTSGEV RLSDFLLWQT SHSCLVFQPV LWPEYTFWNL
FEAILQFQMN HSVLQQKARD MYAEERKRQQ LERDQATVTE QLLREGLQAS GDAQLRRTRL
HKLSARREER VQGFLQALEL KRADWLARLG TASA*

mutated AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNKCFL NVCFAYTSRH EISNAVREMA WGVEQGLLDP
SDISESLLDK CLYTNRSPHP DILIRTSGEV RLSDFLLWQT SHSCLVFQPV LWPEYTFWNL
FEAILQFQMN HSMLQQKARD MYAEERKRQQ LERDQATVTE QLLREGLQAS GDAQLRRTRL
HKLSARREER VQGFLQALEL KRADWLARLG TASA*

speed

0.99 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: 0.999999999998222 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:26786627G>AN/A show variant in all transcripts IGV

HGNC symbol

DHDDS

Ensembl transcript ID

ENST00000525682

Genbank transcript ID

N/A

UniProt peptide

Q86SQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.655G>A
cDNA.748G>A
g.27855G>A

AA changes

V219M Score: 21 explain score(s)

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

219

frameshift

known variant

Reference ID: rs3816539

database	homozygous (A/A)	heterozygous	allele carriers
1000G	574	1132	1706
ExAC	7285	18197	25482

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.335	0.031
	0.028	0.032
(flanking)	0.598	0.1

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
Donor increased	27847	wt: 0.45 / mu: 0.60	wt: GATGAACCATAGCGT mu: GATGAACCATAGCAT	TGAA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

219

mutated

all conserved

219

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022426

253

Fcatus

not conserved

ENSFCAG00000012811

253

Mmusculus

not conserved

ENSMUSG00000012117

253

Ggallus

not conserved

ENSGALG00000000385

253

Trubripes

not conserved

ENSTRUG00000007224

253

Drerio

not conserved

ENSDARG00000039851

253

Dmelanogaster

not conserved

FBgn0029980

253

QRDRWQLDDFRRAER

Celegans

not conserved

T01G1.4

266

Xtropicalis

not conserved

ENSXETG00000012322

255

protein features

start (aa)	end (aa)	feature	details
277	277	CONFLICT	V -> E (in Ref. 6; AAH34152).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

900 / 900

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

300 / 300

position of stopcodon in wt / mu cDNA

993 / 993

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

94 / 94

chromosome

strand

last intron/exon boundary

757

theoretical NMD boundary in CDS

613

length of CDS

900

coding sequence (CDS) position

655

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

748

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

27855

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

26786627

original gDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGGTAAGAAAGAGT

altered gDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGGTAAGAAAGAGT

original cDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGAAGGCCCGAGAC

altered cDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGAAGGCCCGAGAC

wildtype AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNNDIS ESLLDKCLYT NRSPHPDILI RTSGEVRLSD
FLLWQTSHSC LVFQPVLWPE YTFWNLFEAI LQFQMNHSVL QKARDMYAEE RKRQQLERDQ
ATVTEQLLRE GLQASGDAQL RRTRLHKLSA RREERVQGFL QALELKRADW LARLGTASA*

mutated AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNNDIS ESLLDKCLYT NRSPHPDILI RTSGEVRLSD
FLLWQTSHSC LVFQPVLWPE YTFWNLFEAI LQFQMNHSML QKARDMYAEE RKRQQLERDQ
ATVTEQLLRE GLQASGDAQL RRTRLHKLSA RREERVQGFL QALELKRADW LARLGTASA*

speed

1.04 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998222 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:26786627G>AN/A show variant in all transcripts IGV

HGNC symbol

DHDDS

Ensembl transcript ID

ENST00000236342

Genbank transcript ID

NM_205861

UniProt peptide

Q86SQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.757G>A
cDNA.850G>A
g.27855G>A

AA changes

V253M Score: 21 explain score(s)

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

253

frameshift

known variant

Reference ID: rs3816539

database	homozygous (A/A)	heterozygous	allele carriers
1000G	574	1132	1706
ExAC	7285	18197	25482

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.335	0.031
	0.028	0.032
(flanking)	0.598	0.1

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
Donor increased	27847	wt: 0.45 / mu: 0.60	wt: GATGAACCATAGCGT mu: GATGAACCATAGCAT	TGAA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

253

mutated

all conserved

253

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022426

253

Fcatus

not conserved

ENSFCAG00000012811

254

Mmusculus

not conserved

ENSMUSG00000012117

253

Ggallus

not conserved

ENSGALG00000000385

253

Trubripes

not conserved

ENSTRUG00000007224

253

Drerio

not conserved

ENSDARG00000039851

253

Dmelanogaster

not conserved

FBgn0029980

253

QRDRWQLDDFRRAER

Celegans

not conserved

T01G1.4

266

Xtropicalis

not conserved

ENSXETG00000012322

255

protein features

start (aa)	end (aa)	feature	details
277	277	CONFLICT	V -> E (in Ref. 6; AAH34152).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1002 / 1002

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

334 / 334

position of stopcodon in wt / mu cDNA

1095 / 1095

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

94 / 94

chromosome

strand

last intron/exon boundary

859

theoretical NMD boundary in CDS

715

length of CDS

1002

coding sequence (CDS) position

757

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

850

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

27855

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

26786627

original gDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGGTAAGAAAGAGT

altered gDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGGTAAGAAAGAGT

original cDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGAAGGCCCGAGAC

altered cDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGAAGGCCCGAGAC

wildtype AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNKCFL NVCFAYTSRH EISNAVREMA WGVEQGLLDP
SDISESLLDK CLYTNRSPHP DILIRTSGEV RLSDFLLWQT SHSCLVFQPV LWPEYTFWNL
FEAILQFQMN HSVLQKARDM YAEERKRQQL ERDQATVTEQ LLREGLQASG DAQLRRTRLH
KLSARREERV QGFLQALELK RADWLARLGT ASA*

mutated AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKEK LQKHGVCIRV
LGDLHLLPLD LQELIAQAVQ ATKNYNKCFL NVCFAYTSRH EISNAVREMA WGVEQGLLDP
SDISESLLDK CLYTNRSPHP DILIRTSGEV RLSDFLLWQT SHSCLVFQPV LWPEYTFWNL
FEAILQFQMN HSMLQKARDM YAEERKRQQL ERDQATVTEQ LLREGLQASG DAQLRRTRLH
KLSARREERV QGFLQALELK RADWLARLGT ASA*

speed

1.07 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998222 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:26786627G>AN/A show variant in all transcripts IGV

HGNC symbol

DHDDS

Ensembl transcript ID

ENST00000526219

Genbank transcript ID

N/A

UniProt peptide

Q86SQ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.640G>A
cDNA.732G>A
g.27855G>A

AA changes

V214M Score: 21 explain score(s)

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

214

frameshift

known variant

Reference ID: rs3816539

database	homozygous (A/A)	heterozygous	allele carriers
1000G	574	1132	1706
ExAC	7285	18197	25482

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.335	0.031
	0.028	0.032
(flanking)	0.598	0.1

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
Donor increased	27847	wt: 0.45 / mu: 0.60	wt: GATGAACCATAGCGT mu: GATGAACCATAGCAT	TGAA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

214

mutated

all conserved

214

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022426

253

Fcatus

not conserved

ENSFCAG00000012811

253

Mmusculus

not conserved

ENSMUSG00000012117

253

Ggallus

not conserved

ENSGALG00000000385

253

Trubripes

not conserved

ENSTRUG00000007224

253

Drerio

not conserved

ENSDARG00000039851

253

Dmelanogaster

not conserved

FBgn0029980

253

QRDRWQLDDFRRAER

Celegans

not conserved

T01G1.4

266

Xtropicalis

not conserved

ENSXETG00000012322

255

protein features

start (aa)	end (aa)	feature	details
277	277	CONFLICT	V -> E (in Ref. 6; AAH34152).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

885 / 885

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

295 / 295

position of stopcodon in wt / mu cDNA

977 / 977

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

93 / 93

chromosome

strand

last intron/exon boundary

741

theoretical NMD boundary in CDS

598

length of CDS

885

coding sequence (CDS) position

640

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

732

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

27855

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

26786627

original gDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGGTAAGAAAGAGT

altered gDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGGTAAGAAAGAGT

original cDNA sequence snippet

AGTTCCAGATGAACCATAGCGTGCTTCAGAAGGCCCGAGAC

altered cDNA sequence snippet

AGTTCCAGATGAACCATAGCATGCTTCAGAAGGCCCGAGAC

wildtype AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKCF LNVCFAYTSR
HEISNAVREM AWGVEQGLLD PSDISESLLD KCLYTNRSPH PDILIRTSGE VRLSDFLLWQ
TSHSCLVFQP VLWPEYTFWN LFEAILQFQM NHSVLQKARD MYAEERKRQQ LERDQATVTE
QLLREGLQAS GDAQLRRTRL HKLSARREER VQGFLQALEL KRADWLARLG TASA*

mutated AA sequence

MSWIKEGELS LWERFCANII KAGPMPKHIA FIMDGNRRYA KKCQVERQEG HSQGFNKLAE
TLRWCLNLGI LEVTVYAFSI ENFKRSKSEV DGLMDLARQK FSRLMEEKCF LNVCFAYTSR
HEISNAVREM AWGVEQGLLD PSDISESLLD KCLYTNRSPH PDILIRTSGE VRLSDFLLWQ
TSHSCLVFQP VLWPEYTFWN LFEAILQFQM NHSMLQKARD MYAEERKRQQ LERDQATVTE
QLLREGLQAS GDAQLRRTRL HKLSARREER VQGFLQALEL KRADWLARLG TASA*

speed

1.03 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems