MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000405086
Querying Taster for transcript #2: ENST00000451013
MT speed 0 s - this script 3.570463 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GTF2IRD2	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		H514N	single base exchange	rs187868539		show file
GTF2IRD2	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		H61N	single base exchange	rs187868539		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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)

chr7:74212311G>TN/A show variant in all transcripts IGV

HGNC symbol

GTF2IRD2

Ensembl transcript ID

ENST00000405086

Genbank transcript ID

NM_173537

UniProt peptide

Q86UP8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1540C>A
cDNA.1730C>A
g.55537C>A

AA changes

H514N Score: 68 explain score(s)

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

514

frameshift

known variant

Reference ID: rs187868539

database	homozygous (T/T)	heterozygous	allele carriers
1000G	2110	270	2380
ExAC	8054	154	8208

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.144	0.001
	-1.187	0
(flanking)	-1.236	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	55533	0.60	mu: GTGTTTGCAAACCCA	GTTT\|gcaa

distance from splice site

294

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

514

mutated

all conserved

514

Ptroglodytes

all conserved

ENSPTRG00000019295

514

Mmulatta

all conserved

ENSMMUG00000017270

509

Fcatus

all conserved

ENSFCAG00000002626

223

Mmusculus

all conserved

ENSMUSG00000015942

510

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
716	716	CONFLICT	R -> C (in Ref. 5; CAD38861).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2850 / 2850

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

950 / 950

position of stopcodon in wt / mu cDNA

3040 / 3040

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

191 / 191

chromosome

strand

-1

last intron/exon boundary

1437

theoretical NMD boundary in CDS

1196

length of CDS

2850

coding sequence (CDS) position

1540

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

1730

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

55537

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

74212311

original gDNA sequence snippet

AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA

altered gDNA sequence snippet

AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA

original cDNA sequence snippet

AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA

altered cDNA sequence snippet

AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA

wildtype AA sequence

MAQVAVSTLP VEEESSSETR MVVTFLVSAL ESMCKELAKS KAEVACIAVY ETDVFVVGTE
RGCAFVNART DFQKDFAKYC VAEGLCEVKP PCPVNGMQVH SGETEILRKA VEDYFCFCYG
KALGTTVMVP VPYEKMLRDQ SAVVVQGLPE GVAFQHPENY DLATLKWILE NKAGISFIIN
RPFLGPESQL GGPGMVTDAE RSIVSPSESC GPINVKTEPM EDSGISLKAE AVSVKKESED
PNYYQYNMQG SHPSSTSNEV IEMELPMEDS TPLVPSEEPN EDPEAEVKIE GNTNSSSVTN
SAAGVEDLNI VQVTVPDNEK ERLSSIEKIK QLREQVNDLF SRKFGEAIGV DFPVKVPYRK
ITFNPGCVVI DGMPPGVVFK APGYLEISSM RRILEAAEFI KFTVIRPLPG LELSNVGKRK
IDQEGRVFQE KWERAYFFVE VQNIPTCLIC KQSMSVSKEY NLRRHYQTNH SKHYDQYMER
MRDEKLHELK KGLRKYLLGL SDTECPEQKQ VFAHPSPTQK SPVQPVEDLA GNLWEKLREK
IRSFVAYSIA IDEITDINNT TQLAIFIRGV DENFDVSEEL LDTVPMTGTK SGNEIFSRVE
KSLKKFCIDW SKLVSVASTG TPAMVDANNG LVTKLKSRVA TFCKGAELKS ICCIIHPESL
CAQKLKMDHV MDVVVKSVNW ICSRGLNHSE FTTLLYELDS QYGSLLYYTE IKWLSRGLVL
KRFFESLEEI DSFMSSRGKP LPQLSSIDWI RDLAFLVDMT MHLNALNISL QGHSQIVTQM
YDLIRAFLAK LCLWETHLTR NNLAHFPTLK LASRNESDGL NYIPKIAELK TEFQKRLSDF
KLYESELTLF SSPFSTKIDS VHEELQMEVI DLQCNTVLKT KYDKVGIPEF YKYLWGSYPK
YKHHCAKILS MFGSTYICEQ LFSIMKLSKT KYCSQLKDSQ WDSVLHIAT*

mutated AA sequence

MAQVAVSTLP VEEESSSETR MVVTFLVSAL ESMCKELAKS KAEVACIAVY ETDVFVVGTE
RGCAFVNART DFQKDFAKYC VAEGLCEVKP PCPVNGMQVH SGETEILRKA VEDYFCFCYG
KALGTTVMVP VPYEKMLRDQ SAVVVQGLPE GVAFQHPENY DLATLKWILE NKAGISFIIN
RPFLGPESQL GGPGMVTDAE RSIVSPSESC GPINVKTEPM EDSGISLKAE AVSVKKESED
PNYYQYNMQG SHPSSTSNEV IEMELPMEDS TPLVPSEEPN EDPEAEVKIE GNTNSSSVTN
SAAGVEDLNI VQVTVPDNEK ERLSSIEKIK QLREQVNDLF SRKFGEAIGV DFPVKVPYRK
ITFNPGCVVI DGMPPGVVFK APGYLEISSM RRILEAAEFI KFTVIRPLPG LELSNVGKRK
IDQEGRVFQE KWERAYFFVE VQNIPTCLIC KQSMSVSKEY NLRRHYQTNH SKHYDQYMER
MRDEKLHELK KGLRKYLLGL SDTECPEQKQ VFANPSPTQK SPVQPVEDLA GNLWEKLREK
IRSFVAYSIA IDEITDINNT TQLAIFIRGV DENFDVSEEL LDTVPMTGTK SGNEIFSRVE
KSLKKFCIDW SKLVSVASTG TPAMVDANNG LVTKLKSRVA TFCKGAELKS ICCIIHPESL
CAQKLKMDHV MDVVVKSVNW ICSRGLNHSE FTTLLYELDS QYGSLLYYTE IKWLSRGLVL
KRFFESLEEI DSFMSSRGKP LPQLSSIDWI RDLAFLVDMT MHLNALNISL QGHSQIVTQM
YDLIRAFLAK LCLWETHLTR NNLAHFPTLK LASRNESDGL NYIPKIAELK TEFQKRLSDF
KLYESELTLF SSPFSTKIDS VHEELQMEVI DLQCNTVLKT KYDKVGIPEF YKYLWGSYPK
YKHHCAKILS MFGSTYICEQ LFSIMKLSKT KYCSQLKDSQ WDSVLHIAT*

speed

0.78 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: 0.999999999999999 (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)

chr7:74212311G>TN/A show variant in all transcripts IGV

HGNC symbol

GTF2IRD2

Ensembl transcript ID

ENST00000451013

Genbank transcript ID

N/A

UniProt peptide

Q86UP8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.181C>A
cDNA.421C>A
g.55537C>A

AA changes

H61N Score: 68 explain score(s)

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

frameshift

known variant

Reference ID: rs187868539

database	homozygous (T/T)	heterozygous	allele carriers
1000G	2110	270	2380
ExAC	8054	154	8208

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.144	0.001
	-1.187	0
(flanking)	-1.236	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	55533	0.60	mu: GTGTTTGCAAACCCA	GTTT\|gcaa

distance from splice site

294

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000019295

514

Mmulatta

all conserved

ENSMMUG00000017270

509

Fcatus

all conserved

ENSFCAG00000002626

223

Mmusculus

all conserved

ENSMUSG00000015942

508

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
98	192	REPEAT	GTF2I-like 1.	might get lost (downstream of altered splice site)
323	417	REPEAT	GTF2I-like 2.	might get lost (downstream of altered splice site)
500	500	CONFLICT	L -> S (in Ref. 4; BAF84120).	might get lost (downstream of altered splice site)
716	716	CONFLICT	R -> C (in Ref. 5; CAD38861).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1491 / 1491

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

497 / 497

position of stopcodon in wt / mu cDNA

1731 / 1731

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

241 / 241

chromosome

strand

-1

last intron/exon boundary

128

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1491

coding sequence (CDS) position

181

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

421

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

55537

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

74212311

original gDNA sequence snippet

AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA

altered gDNA sequence snippet

AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA

original cDNA sequence snippet

AGCAAAAACAAGTGTTTGCACACCCAAGTCCAACCCAGAAA

altered cDNA sequence snippet

AGCAAAAACAAGTGTTTGCAAACCCAAGTCCAACCCAGAAA

wildtype AA sequence

MSVSKEYNLR RHYQTNHSKH YDQYMERMRD EKLHELKKGL RKYLLGLSDT ECPEQKQVFA
HPSPTQKSPV QPVEDLAGNL WEKLREKIRS FVAYSIAIDE ITDINNTTQL AIFIRGVDEN
FDVSEELLDT VPMTGTKSGN EIFSRVEKSL KKFCIDWSKL VSVASTGTPA MVDANNGLVT
KLKSRVATFC KGAELKSICC IIHPESLCAQ KLKMDHVMDV VVKSVNWICS RGLNHSEFTT
LLYELDSQYG SLLYYTEIKW LSRGLVLKRF FESLEEIDSF MSSRGKPLPQ LSSIDWIRDL
AFLVDMTMHL NALNISLQGH SQIVTQMYDL IRAFLAKLCL WETHLTRNNL AHFPTLKLAS
RNESDGLNYI PKIAELKTEF QKRLSDFKLY ESELTLFSSP FSTKIDSVHE ELQMEVIDLQ
CNTVLKTKYD KVGIPEFYKY LWGSYPKYKH HCAKILSMFG STYICEQLFS IMKLSKTKYC
SQLKDSQWDS VLHIAT*

mutated AA sequence

MSVSKEYNLR RHYQTNHSKH YDQYMERMRD EKLHELKKGL RKYLLGLSDT ECPEQKQVFA
NPSPTQKSPV QPVEDLAGNL WEKLREKIRS FVAYSIAIDE ITDINNTTQL AIFIRGVDEN
FDVSEELLDT VPMTGTKSGN EIFSRVEKSL KKFCIDWSKL VSVASTGTPA MVDANNGLVT
KLKSRVATFC KGAELKSICC IIHPESLCAQ KLKMDHVMDV VVKSVNWICS RGLNHSEFTT
LLYELDSQYG SLLYYTEIKW LSRGLVLKRF FESLEEIDSF MSSRGKPLPQ LSSIDWIRDL
AFLVDMTMHL NALNISLQGH SQIVTQMYDL IRAFLAKLCL WETHLTRNNL AHFPTLKLAS
RNESDGLNYI PKIAELKTEF QKRLSDFKLY ESELTLFSSP FSTKIDSVHE ELQMEVIDLQ
CNTVLKTKYD KVGIPEFYKY LWGSYPKYKH HCAKILSMFG STYICEQLFS IMKLSKTKYC
SQLKDSQWDS VLHIAT*

speed

0.79 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems