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: ENST00000360639
Querying Taster for transcript #2: ENST00000394987
Querying Taster for transcript #3: ENST00000567617
MT speed 0 s - this script 6.689724 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C15orf39	polymorphism_automatic	2.4293012046428e-11	simple_aae		affected		S536A	single base exchange	rs28509789		show file
C15orf39	polymorphism_automatic	2.4293012046428e-11	simple_aae		affected		S536A	single base exchange	rs28509789		show file
C15orf39	polymorphism_automatic	2.4293012046428e-11	simple_aae		affected		S536A	single base exchange	rs28509789		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975707 (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)

chr15:75499995T>GN/A show variant in all transcripts IGV

HGNC symbol

C15orf39

Ensembl transcript ID

ENST00000360639

Genbank transcript ID

N/A

UniProt peptide

Q6ZRI6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1606T>G
cDNA.1926T>G
g.12012T>G

AA changes

S536A Score: 99 explain score(s)

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

536

frameshift

known variant

Reference ID: rs28509789

database	homozygous (G/G)	heterozygous	allele carriers
1000G	414	1137	1551
ExAC	6405	19957	26362

regulatory features

H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.031	0
	-0.189	0
(flanking)	-0.149	0

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 gained	12006	0.68	mu: CTGAGCCTGACGCAG	GAGC\|ctga

distance from splice site

1171

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

536

mutated

all conserved

536

Ptroglodytes

all identical

ENSPTRG00000007294

536

Mmulatta

all identical

ENSMMUG00000008529

530

Fcatus

all identical

ENSFCAG00000012917

536

Mmusculus

all identical

ENSMUSG00000032300

526

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069168

590

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
592	592	CONFLICT	R -> H (in Ref. 7; CAD39045).	might get lost (downstream of altered splice site)
913	913	CONFLICT	L -> P (in Ref. 3; BAC87324).	might get lost (downstream of altered splice site)
936	936	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3144 / 3144

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

1048 / 1048

position of stopcodon in wt / mu cDNA

3464 / 3464

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

321 / 321

chromosome

strand

last intron/exon boundary

3097

theoretical NMD boundary in CDS

2726

length of CDS

3144

coding sequence (CDS) position

1606

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

1926

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

12012

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

75499995

original gDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered gDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

original cDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered cDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

wildtype AA sequence

MAEKRPLRTL GPVMYGKLPR LETDSGLEHS LPHSVGNQDP CTYKGSYFSC PMAGTPKAES
EQLASWTPYP PLYSTGMAGP PLQADNLLTN CLFYRSPAEG PEKMQDSSPV ELLPFSPQAH
SYPGPPLAAP KPVYRNPLCY GLSTCLGEGA VKRPLDVDWT LATGPLLPSA DPPCSLAPAP
SKGQTLDGTF LRGVPAEGSS KDSSGSFSPC QPFLEKYQTI HSTGFLASRY TGPYPRNSKQ
AMSEGPSSPW TQLAQPLGPP CQDTGPTHYP PPHHPPPHPP QALPCPPACR HPEKQGSYSP
ALPLQPLGGH KGTGYQAGGL GSPYLRQQAA QAPYIPPLGL DAYPYPSAPL PAPSPGLKLE
PPLTPRCPLD FAPQTLSFPY ARDDLSLYGA SPGLGGTPPS QNNVRAVPQP GAFQRACQPL
PASQPCSEPV RPAQEAEEKT WLPSCRKEKL QPRLSEHSGP PIVIRDSPVP CTPPALPPCA
RECQSLPQKE GARPPSSPPM PVIDNVFSLA PYRDYLDVPA PEATTEPDSA TAEPDSAPAT
SEGQDKGCRG TLPAQEGPSG SKPLRGSLKE EVALDLSVRK PTAEASPVKA SRSVEHAKPT
AAMDVPDVGN MVSDLPGLKK IDTEAPGLPG VPVTTDAMPR TNFHSSVAFM FRKFKILRPA
PLPAAVVPST PTSAPAPTQP APTPTSGPIG LRILAQQPLS VTCFSLALPS PPAVAVASPA
PAPAPSPAPA RAQAPASARD PAPAPAPVAG PAPASTSAPG DSLEQHFTGL HASLCDAISG
SVAHSPPEKL REWLETAGPW GQAAWQDCQG VQGLLAKLLS QLQRFDRTHR CPFPHVVRAG
AIFVPIHLVK ERLFPRLPPA SVDHVLQEHR VELRPTTLSE ERALRELALP GCTSRMLKLL
ALRQLPDIYP DLLGLQWRDC VRRQLGDFDT EAGAVSSSEP TVARGEPESL ALAQKSPAPK
VRKPGRKPPT PGPEKAEAAA GEESCGASPT PATSASPPGP TLKARFRSLL ETAWLNGLAL
PTWGHKSSRP DQPSPCPQLL DSQSHHL*

mutated AA sequence

MAEKRPLRTL GPVMYGKLPR LETDSGLEHS LPHSVGNQDP CTYKGSYFSC PMAGTPKAES
EQLASWTPYP PLYSTGMAGP PLQADNLLTN CLFYRSPAEG PEKMQDSSPV ELLPFSPQAH
SYPGPPLAAP KPVYRNPLCY GLSTCLGEGA VKRPLDVDWT LATGPLLPSA DPPCSLAPAP
SKGQTLDGTF LRGVPAEGSS KDSSGSFSPC QPFLEKYQTI HSTGFLASRY TGPYPRNSKQ
AMSEGPSSPW TQLAQPLGPP CQDTGPTHYP PPHHPPPHPP QALPCPPACR HPEKQGSYSP
ALPLQPLGGH KGTGYQAGGL GSPYLRQQAA QAPYIPPLGL DAYPYPSAPL PAPSPGLKLE
PPLTPRCPLD FAPQTLSFPY ARDDLSLYGA SPGLGGTPPS QNNVRAVPQP GAFQRACQPL
PASQPCSEPV RPAQEAEEKT WLPSCRKEKL QPRLSEHSGP PIVIRDSPVP CTPPALPPCA
RECQSLPQKE GARPPSSPPM PVIDNVFSLA PYRDYLDVPA PEATTEPDSA TAEPDAAPAT
SEGQDKGCRG TLPAQEGPSG SKPLRGSLKE EVALDLSVRK PTAEASPVKA SRSVEHAKPT
AAMDVPDVGN MVSDLPGLKK IDTEAPGLPG VPVTTDAMPR TNFHSSVAFM FRKFKILRPA
PLPAAVVPST PTSAPAPTQP APTPTSGPIG LRILAQQPLS VTCFSLALPS PPAVAVASPA
PAPAPSPAPA RAQAPASARD PAPAPAPVAG PAPASTSAPG DSLEQHFTGL HASLCDAISG
SVAHSPPEKL REWLETAGPW GQAAWQDCQG VQGLLAKLLS QLQRFDRTHR CPFPHVVRAG
AIFVPIHLVK ERLFPRLPPA SVDHVLQEHR VELRPTTLSE ERALRELALP GCTSRMLKLL
ALRQLPDIYP DLLGLQWRDC VRRQLGDFDT EAGAVSSSEP TVARGEPESL ALAQKSPAPK
VRKPGRKPPT PGPEKAEAAA GEESCGASPT PATSASPPGP TLKARFRSLL ETAWLNGLAL
PTWGHKSSRP DQPSPCPQLL DSQSHHL*

speed

0.90 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: 0.999999999975707 (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)

chr15:75499995T>GN/A show variant in all transcripts IGV

HGNC symbol

C15orf39

Ensembl transcript ID

ENST00000394987

Genbank transcript ID

NM_015492

UniProt peptide

Q6ZRI6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1606T>G
cDNA.1839T>G
g.12012T>G

AA changes

S536A Score: 99 explain score(s)

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

536

frameshift

known variant

Reference ID: rs28509789

database	homozygous (G/G)	heterozygous	allele carriers
1000G	414	1137	1551
ExAC	6405	19957	26362

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.031	0
	-0.189	0
(flanking)	-0.149	0

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 gained	12006	0.68	mu: CTGAGCCTGACGCAG	GAGC\|ctga

distance from splice site

1171

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

536

mutated

all conserved

536

Ptroglodytes

all identical

ENSPTRG00000007294

536

Mmulatta

all identical

ENSMMUG00000008529

530

Fcatus

all identical

ENSFCAG00000012917

536

Mmusculus

all identical

ENSMUSG00000032300

526

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069168

590

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
592	592	CONFLICT	R -> H (in Ref. 7; CAD39045).	might get lost (downstream of altered splice site)
913	913	CONFLICT	L -> P (in Ref. 3; BAC87324).	might get lost (downstream of altered splice site)
936	936	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3144 / 3144

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

1048 / 1048

position of stopcodon in wt / mu cDNA

3377 / 3377

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

234 / 234

chromosome

strand

last intron/exon boundary

3010

theoretical NMD boundary in CDS

2726

length of CDS

3144

coding sequence (CDS) position

1606

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

1839

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

12012

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

75499995

original gDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered gDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

original cDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered cDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

wildtype AA sequence

mutated AA sequence

MAEKRPLRTL GPVMYGKLPR LETDSGLEHS LPHSVGNQDP CTYKGSYFSC PMAGTPKAES
EQLASWTPYP PLYSTGMAGP PLQADNLLTN CLFYRSPAEG PEKMQDSSPV ELLPFSPQAH
SYPGPPLAAP KPVYRNPLCY GLSTCLGEGA VKRPLDVDWT LATGPLLPSA DPPCSLAPAP
SKGQTLDGTF LRGVPAEGSS KDSSGSFSPC QPFLEKYQTI HSTGFLASRY TGPYPRNSKQ
AMSEGPSSPW TQLAQPLGPP CQDTGPTHYP PPHHPPPHPP QALPCPPACR HPEKQGSYSP
ALPLQPLGGH KGTGYQAGGL GSPYLRQQAA QAPYIPPLGL DAYPYPSAPL PAPSPGLKLE
PPLTPRCPLD FAPQTLSFPY ARDDLSLYGA SPGLGGTPPS QNNVRAVPQP GAFQRACQPL
PASQPCSEPV RPAQEAEEKT WLPSCRKEKL QPRLSEHSGP PIVIRDSPVP CTPPALPPCA
RECQSLPQKE GARPPSSPPM PVIDNVFSLA PYRDYLDVPA PEATTEPDSA TAEPDAAPAT
SEGQDKGCRG TLPAQEGPSG SKPLRGSLKE EVALDLSVRK PTAEASPVKA SRSVEHAKPT
AAMDVPDVGN MVSDLPGLKK IDTEAPGLPG VPVTTDAMPR TNFHSSVAFM FRKFKILRPA
PLPAAVVPST PTSAPAPTQP APTPTSGPIG LRILAQQPLS VTCFSLALPS PPAVAVASPA
PAPAPSPAPA RAQAPASARD PAPAPAPVAG PAPASTSAPG DSLEQHFTGL HASLCDAISG
SVAHSPPEKL REWLETAGPW GQAAWQDCQG VQGLLAKLLS QLQRFDRTHR CPFPHVVRAG
AIFVPIHLVK ERLFPRLPPA SVDHVLQEHR VELRPTTLSE ERALRELALP GCTSRMLKLL
ALRQLPDIYP DLLGLQWRDC VRRQLGDFDT EAGAVSSSEP TVARGEPESL ALAQKSPAPK
VRKPGRKPPT PGPEKAEAAA GEESCGASPT PATSASPPGP TLKARFRSLL ETAWLNGLAL
PTWGHKSSRP DQPSPCPQLL DSQSHHL*

speed

1.25 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975707 (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)

chr15:75499995T>GN/A show variant in all transcripts IGV

HGNC symbol

C15orf39

Ensembl transcript ID

ENST00000567617

Genbank transcript ID

N/A

UniProt peptide

Q6ZRI6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1606T>G
cDNA.1606T>G
g.12012T>G

AA changes

S536A Score: 99 explain score(s)

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

536

frameshift

known variant

Reference ID: rs28509789

database	homozygous (G/G)	heterozygous	allele carriers
1000G	414	1137	1551
ExAC	6405	19957	26362

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.031	0
	-0.189	0
(flanking)	-0.149	0

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 gained	12006	0.68	mu: CTGAGCCTGACGCAG	GAGC\|ctga

distance from splice site

1223

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

536

mutated

all conserved

536

Ptroglodytes

all identical

ENSPTRG00000007294

536

Mmulatta

all identical

ENSMMUG00000008529

530

Fcatus

all identical

ENSFCAG00000012917

536

Mmusculus

all identical

ENSMUSG00000032300

526

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069168

590

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
592	592	CONFLICT	R -> H (in Ref. 7; CAD39045).	might get lost (downstream of altered splice site)
913	913	CONFLICT	L -> P (in Ref. 3; BAC87324).	might get lost (downstream of altered splice site)
936	936	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2817 / 2817

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

939 / 939

position of stopcodon in wt / mu cDNA

2817 / 2817

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

2829

theoretical NMD boundary in CDS

2778

length of CDS

2817

coding sequence (CDS) position

1606

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

1606

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

12012

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

75499995

original gDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered gDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

original cDNA sequence snippet

CTGCCACAGCTGAGCCTGACTCAGCCCCAGCCACCAGTGAA

altered cDNA sequence snippet

CTGCCACAGCTGAGCCTGACGCAGCCCCAGCCACCAGTGAA

wildtype AA sequence

mutated AA sequence

MAEKRPLRTL GPVMYGKLPR LETDSGLEHS LPHSVGNQDP CTYKGSYFSC PMAGTPKAES
EQLASWTPYP PLYSTGMAGP PLQADNLLTN CLFYRSPAEG PEKMQDSSPV ELLPFSPQAH
SYPGPPLAAP KPVYRNPLCY GLSTCLGEGA VKRPLDVDWT LATGPLLPSA DPPCSLAPAP
SKGQTLDGTF LRGVPAEGSS KDSSGSFSPC QPFLEKYQTI HSTGFLASRY TGPYPRNSKQ
AMSEGPSSPW TQLAQPLGPP CQDTGPTHYP PPHHPPPHPP QALPCPPACR HPEKQGSYSP
ALPLQPLGGH KGTGYQAGGL GSPYLRQQAA QAPYIPPLGL DAYPYPSAPL PAPSPGLKLE
PPLTPRCPLD FAPQTLSFPY ARDDLSLYGA SPGLGGTPPS QNNVRAVPQP GAFQRACQPL
PASQPCSEPV RPAQEAEEKT WLPSCRKEKL QPRLSEHSGP PIVIRDSPVP CTPPALPPCA
RECQSLPQKE GARPPSSPPM PVIDNVFSLA PYRDYLDVPA PEATTEPDSA TAEPDAAPAT
SEGQDKGCRG TLPAQEGPSG SKPLRGSLKE EVALDLSVRK PTAEASPVKA SRSVEHAKPT
AAMDVPDVGN MVSDLPGLKK IDTEAPGLPG VPVTTDAMPR TNFHSSVAFM FRKFKILRPA
PLPAAVVPST PTSAPAPTQP APTPTSGPIG LRILAQQPLS VTCFSLALPS PPAVAVASPA
PAPAPSPAPA RAQAPASARD PAPAPAPVAG PAPASTSAPG DSLEQHFTGL HASLCDAISG
SVAHSPPEKL REWLETAGPW GQAAWQDCQG VQGLLAKLLS QLQRFDRTHR CPFPHVVRAG
AIFVPIHLVK ERLFPRLPPA SVDHVLQEHR VELRPTTLSE ERALRELALP GCTSRMLKLL
ALRQLPDIYP DLLGLQWRDC VRRQLGEHGA APVATGAV*

speed

0.94 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