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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000413272
Querying Taster for transcript #2: ENST00000341513
MT speed 1.34 s - this script 3.36087 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NUGGC	polymorphism_automatic	0.010158675384747	simple_aae		affected		S474N	single base exchange	rs13279787		show file
NUGGC	polymorphism_automatic	0.010158675384747	simple_aae		affected		S474N	single base exchange	rs13279787		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.989841324615253 (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)

chr8:27903069C>TN/A show variant in all transcripts IGV

HGNC symbol

NUGGC

Ensembl transcript ID

ENST00000413272

Genbank transcript ID

NM_001010906

UniProt peptide

Q68CJ6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1421G>A
cDNA.1564G>A
g.38320G>A

AA changes

S474N Score: 46 explain score(s)

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

474

frameshift

known variant

Reference ID: rs13279787

database	homozygous (T/T)	heterozygous	allele carriers
1000G	358	1178	1536
ExAC	7570	17627	25197

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.496	0.877
	0.425	0.893
(flanking)	0.313	0.914

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	38315	wt: 0.75 / mu: 0.95	wt: CTCACAGATAGTTTC mu: CTCACAGATAATTTC	CACA\|gata
Donor increased	38321	wt: 0.38 / mu: 0.53	wt: GATAGTTTCAACTCC mu: GATAATTTCAACTCC	TAGT\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

474

mutated

all conserved

474

Ptroglodytes

all identical

ENSPTRG00000020114

473

Mmulatta

all identical

ENSMMUG00000001040

476

Fcatus

all identical

ENSFCAG00000002892

459

Mmusculus

all conserved

ENSMUSG00000061356

490

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091951

141

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
745	775	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2391 / 2391

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

797 / 797

position of stopcodon in wt / mu cDNA

2534 / 2534

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

144 / 144

chromosome

strand

-1

last intron/exon boundary

2389

theoretical NMD boundary in CDS

2195

length of CDS

2391

coding sequence (CDS) position

1421

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

1564

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

38320

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

27903069

original gDNA sequence snippet

CCTGTTGCTCCTCACAGATAGTTTCAACTCCACGCAAAACC

altered gDNA sequence snippet

CCTGTTGCTCCTCACAGATAATTTCAACTCCACGCAAAACC

original cDNA sequence snippet

CCTGTTGCTCCTCACAGATAGTTTCAACTCCACGCAAAACC

altered cDNA sequence snippet

CCTGTTGCTCCTCACAGATAATTTCAACTCCACGCAAAACC

wildtype AA sequence

MAETKDVFGQ EPHPVEDDLY KERTRKRRKS DRDQRFRAFP SMEQSALKEY EKLESRTRRV
LSNTYQKLIQ SVFLDDSIPN GVKYLINRLL ALIEKPTVDP IYIALFGSTG AGKSSLINAI
IQQAMFLPVS GESICTSCIV QVSSGCCVQY EAKIHLLSDQ EWREELKNLT KLLHRTEELS
REEADAWNRD EAVEEATWKL QMIYGNGAES KNYEELLRAK PKRKIPTSRV ITLKAEEAEE
LSIKLDPYIR TQRRDWDGEA AEMRIWPLIK HVEVTLPKSD LIPEGVVLVD IPGTGDFNSK
RDEMWKKTID KCSVIWVISD IERVSGGQAH EDLLNESIKA CQRGFCRDVA LVVTKMDKLH
LPEYLRERKA GNQAIQSQRE AVLERNEMIK LQRTRILKEK LKRKLPADFK VLEASDLVYT
VSAQEYWQQA LLTEEETEIP KLREYIRKSL LDKKKRTVTK YVTEAFGLLL LTDSFNSTQN
LPNEHLHMSV LRRFAEEKVE LLEKAIAQCF ACMEQPLQEG VRTARTSYRC ILRACLVRSK
GNQGFHQTLK AVCLKNGIYA SRTLARIDLN EALTQPVYDQ IDPVFGSIFR TGKPTGSALM
PHIDAFKQSL QEKMTEIGIR SGWKYDSCKK NFLIQEISAI LGGLEDHILR RKRRIYESLT
ASVQSDLKLC YEEAAQITGK KACERMKDAI RRGVDRQVAE GMFERAQERM QHQFQQLKTG
IVEKVKGSIT TMLALASSQG DGLYKELADV GSEYKEMEKL HRSLREVAEN ARLRKGMQEF
LLRASPSKAG PPGTSL*

mutated AA sequence

MAETKDVFGQ EPHPVEDDLY KERTRKRRKS DRDQRFRAFP SMEQSALKEY EKLESRTRRV
LSNTYQKLIQ SVFLDDSIPN GVKYLINRLL ALIEKPTVDP IYIALFGSTG AGKSSLINAI
IQQAMFLPVS GESICTSCIV QVSSGCCVQY EAKIHLLSDQ EWREELKNLT KLLHRTEELS
REEADAWNRD EAVEEATWKL QMIYGNGAES KNYEELLRAK PKRKIPTSRV ITLKAEEAEE
LSIKLDPYIR TQRRDWDGEA AEMRIWPLIK HVEVTLPKSD LIPEGVVLVD IPGTGDFNSK
RDEMWKKTID KCSVIWVISD IERVSGGQAH EDLLNESIKA CQRGFCRDVA LVVTKMDKLH
LPEYLRERKA GNQAIQSQRE AVLERNEMIK LQRTRILKEK LKRKLPADFK VLEASDLVYT
VSAQEYWQQA LLTEEETEIP KLREYIRKSL LDKKKRTVTK YVTEAFGLLL LTDNFNSTQN
LPNEHLHMSV LRRFAEEKVE LLEKAIAQCF ACMEQPLQEG VRTARTSYRC ILRACLVRSK
GNQGFHQTLK AVCLKNGIYA SRTLARIDLN EALTQPVYDQ IDPVFGSIFR TGKPTGSALM
PHIDAFKQSL QEKMTEIGIR SGWKYDSCKK NFLIQEISAI LGGLEDHILR RKRRIYESLT
ASVQSDLKLC YEEAAQITGK KACERMKDAI RRGVDRQVAE GMFERAQERM QHQFQQLKTG
IVEKVKGSIT TMLALASSQG DGLYKELADV GSEYKEMEKL HRSLREVAEN ARLRKGMQEF
LLRASPSKAG PPGTSL*

speed

0.82 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: 0.989841324615253 (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)

chr8:27903069C>TN/A show variant in all transcripts IGV

HGNC symbol

NUGGC

Ensembl transcript ID

ENST00000341513

Genbank transcript ID

N/A

UniProt peptide

Q68CJ6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1421G>A
cDNA.1564G>A
g.38320G>A

AA changes

S474N Score: 46 explain score(s)

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

474

frameshift

known variant

Reference ID: rs13279787

database	homozygous (T/T)	heterozygous	allele carriers
1000G	358	1178	1536
ExAC	7570	17627	25197

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.496	0.877
	0.425	0.893
(flanking)	0.313	0.914

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	38315	wt: 0.75 / mu: 0.95	wt: CTCACAGATAGTTTC mu: CTCACAGATAATTTC	CACA\|gata
Donor increased	38321	wt: 0.38 / mu: 0.53	wt: GATAGTTTCAACTCC mu: GATAATTTCAACTCC	TAGT\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

474

mutated

all conserved

474

Ptroglodytes

all identical

ENSPTRG00000020114

473

Mmulatta

all identical

ENSMMUG00000001040

476

Fcatus

all identical

ENSFCAG00000002892

459

Mmusculus

all conserved

ENSMUSG00000061356

490

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091951

141

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
745	775	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2391 / 2391

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

797 / 797

position of stopcodon in wt / mu cDNA

2534 / 2534

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

144 / 144

chromosome

strand

-1

last intron/exon boundary

2389

theoretical NMD boundary in CDS

2195

length of CDS

2391

coding sequence (CDS) position

1421

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

1564

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

38320

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

27903069

original gDNA sequence snippet

CCTGTTGCTCCTCACAGATAGTTTCAACTCCACGCAAAACC

altered gDNA sequence snippet

CCTGTTGCTCCTCACAGATAATTTCAACTCCACGCAAAACC

original cDNA sequence snippet

CCTGTTGCTCCTCACAGATAGTTTCAACTCCACGCAAAACC

altered cDNA sequence snippet

CCTGTTGCTCCTCACAGATAATTTCAACTCCACGCAAAACC

wildtype AA sequence

MAETKDVFGQ EPHPVEDDLY KERTRKRRKS DRDQRFRAFP SMEQSALKEY EKLESRTRRV
LSNTYQKLIQ SVFLDDSIPN GVKYLINRLL ALIEKPTVDP IYIALFGSTG AGKSSLINAI
IQQAMFLPVS GESICTSCIV QVSSGCCVQY EAKIHLLSDQ EWREELKNLT KLLHRTEELS
REEADAWNRD EAVEEATWKL QMIYGNGAES KNYEELLRAK PKRKIPTSRV ITLKAEEAEE
LSIKLDPYIR TQRRDWDGEA AEMRIWPLIK HVEVTLPKSD LIPEGVVLVD IPGTGDFNSK
RDEMWKKTID KCSVIWVISD IERVSGGQAH EDLLNESIKA CQRGFCRDVA LVVTKMDKLH
LPEYLREERK GWQAIQSQRE AVLERNEMIK LQRTRILKEK LKRKLPADFK VLEASDLVYT
VSAQEYWQQA LLTEEETEIP KLREYIRKSL LDKKKRTVTK YVTEAFGLLL LTDSFNSTQN
LPNEHLHMSV LRRFAEEKVE LLEKAIAQCF ACMEQPLQEG VRTARTSYRC ILRACLVRSK
GNQGFHQTLK AVCLKNGIYA SRTLARIDLN EALTQPVYDQ IDPVFGSIFR TGKPTGSALM
PHIDAFKQSL QEKMTEIGIR SGWKYDSCKK NFLIQEISAI LGGLEDHILR RKRRIYESLT
ASVQSDLKLC YEEAAQITGK KACERMKDAI RRGVDRQVAE GMFERAQERM QHQFQQLKTG
IVEKVKGSIT TMLALASSQG DGLYKELADV GSEYKEMEKL HRSLREVAEN ARLRKGMQEF
LLRASPSKAG PPGTSL*

mutated AA sequence

MAETKDVFGQ EPHPVEDDLY KERTRKRRKS DRDQRFRAFP SMEQSALKEY EKLESRTRRV
LSNTYQKLIQ SVFLDDSIPN GVKYLINRLL ALIEKPTVDP IYIALFGSTG AGKSSLINAI
IQQAMFLPVS GESICTSCIV QVSSGCCVQY EAKIHLLSDQ EWREELKNLT KLLHRTEELS
REEADAWNRD EAVEEATWKL QMIYGNGAES KNYEELLRAK PKRKIPTSRV ITLKAEEAEE
LSIKLDPYIR TQRRDWDGEA AEMRIWPLIK HVEVTLPKSD LIPEGVVLVD IPGTGDFNSK
RDEMWKKTID KCSVIWVISD IERVSGGQAH EDLLNESIKA CQRGFCRDVA LVVTKMDKLH
LPEYLREERK GWQAIQSQRE AVLERNEMIK LQRTRILKEK LKRKLPADFK VLEASDLVYT
VSAQEYWQQA LLTEEETEIP KLREYIRKSL LDKKKRTVTK YVTEAFGLLL LTDNFNSTQN
LPNEHLHMSV LRRFAEEKVE LLEKAIAQCF ACMEQPLQEG VRTARTSYRC ILRACLVRSK
GNQGFHQTLK AVCLKNGIYA SRTLARIDLN EALTQPVYDQ IDPVFGSIFR TGKPTGSALM
PHIDAFKQSL QEKMTEIGIR SGWKYDSCKK NFLIQEISAI LGGLEDHILR RKRRIYESLT
ASVQSDLKLC YEEAAQITGK KACERMKDAI RRGVDRQVAE GMFERAQERM QHQFQQLKTG
IVEKVKGSIT TMLALASSQG DGLYKELADV GSEYKEMEKL HRSLREVAEN ARLRKGMQEF
LLRASPSKAG PPGTSL*

speed

0.52 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems