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: ENST00000513449
Querying Taster for transcript #2: ENST00000389737
MT speed 0 s - this script 3.693186 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TRMT44	polymorphism_automatic	1.37889699658444e-11	simple_aae				R111G	single base exchange	rs1880024		show file
TRMT44	polymorphism_automatic	1.37889699658444e-11	simple_aae				R352G	single base exchange	rs1880024		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999986211 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:8454639A>GN/A show variant in all transcripts IGV

HGNC symbol

TRMT44

Ensembl transcript ID

ENST00000513449

Genbank transcript ID

N/A

UniProt peptide

Q8IYL2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.331A>G
cDNA.580A>G
g.16773A>G

AA changes

R111G Score: 125 explain score(s)

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

111

frameshift

known variant

Reference ID: rs1880024

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1452	847	2299
ExAC	4149	2472	6621

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.501	0.113
	0.523	0.108
(flanking)	2.053	0.111

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 marginally increased	16770	wt: 0.8820 / mu: 0.8920 (marginal change - not scored)	wt: CTGAGAGGAGACTAA mu: CTGAGAGGGGACTAA	GAGA\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

111

mutated

not conserved

111

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000006235

123

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029097

308

Ggallus

not conserved

ENSGALG00000015594

270

Trubripes

not conserved

ENSTRUG00000011090

257

Drerio

not conserved

ENSDARG00000033957

250

Dmelanogaster

not conserved

FBgn0037708

213

Celegans

not conserved

C23G10.7

243

Xtropicalis

all conserved

ENSXETG00000030882

267

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1236 / 1236

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

412 / 412

position of stopcodon in wt / mu cDNA

1485 / 1485

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

250 / 250

chromosome

strand

last intron/exon boundary

1021

theoretical NMD boundary in CDS

721

length of CDS

1236

coding sequence (CDS) position

331

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

580

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

16773

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

8454639

original gDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGAGACTAACTGCCAGGCAGTCC

altered gDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGGGACTAACTGCCAGGCAGTCC

original cDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGAGACTAACTGCCAGGCAGTCC

altered cDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGGGACTAACTGCCAGGCAGTCC

wildtype AA sequence

MCIKFSSVIA KKNERWHSDG IVYPKPTWLG EELLAKLAKW SVENKKSDFK STLSLISIMK
YSKAYQELKE KYKEMVKVWP EVTDPEKFVY EDVAIAAYLL ILWEEERAER RLTARQSFVD
LGCGNGLLVH ILSSEGHPGR GIDVRRRKIW DMYGPQTQLE EDAITPNDKT LFPDVDWLIG
NHSDELTPWI PVIAARSSYN CRFFVLPCCF FDFIGRYSRR QSKKTQYREY LDFIKEVGFT
CGFHVDEDCL RIPSTKRVCL VGKSRTYPSS REASVDEKRT QYIKSRRGCP VSPPGWELSP
SPRWVAAGSA GHCDGQQALD ARVGCVTRAW AAEHGAGPQA EGPWLPGFHP REKAERVRNC
AALPRDFIDQ VVLQVANLLL GGKQLNTRSS RNGSLKTWNG GGKLSTILGR G*

mutated AA sequence

MCIKFSSVIA KKNERWHSDG IVYPKPTWLG EELLAKLAKW SVENKKSDFK STLSLISIMK
YSKAYQELKE KYKEMVKVWP EVTDPEKFVY EDVAIAAYLL ILWEEERAER GLTARQSFVD
LGCGNGLLVH ILSSEGHPGR GIDVRRRKIW DMYGPQTQLE EDAITPNDKT LFPDVDWLIG
NHSDELTPWI PVIAARSSYN CRFFVLPCCF FDFIGRYSRR QSKKTQYREY LDFIKEVGFT
CGFHVDEDCL RIPSTKRVCL VGKSRTYPSS REASVDEKRT QYIKSRRGCP VSPPGWELSP
SPRWVAAGSA GHCDGQQALD ARVGCVTRAW AAEHGAGPQA EGPWLPGFHP REKAERVRNC
AALPRDFIDQ VVLQVANLLL GGKQLNTRSS RNGSLKTWNG GGKLSTILGR G*

speed

0.87 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: 0.999999999986211 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:8454639A>GN/A show variant in all transcripts IGV

HGNC symbol

TRMT44

Ensembl transcript ID

ENST00000389737

Genbank transcript ID

NM_152544

UniProt peptide

Q8IYL2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1054A>G
cDNA.1054A>G
g.16773A>G

AA changes

R352G Score: 125 explain score(s)

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

352

frameshift

known variant

Reference ID: rs1880024

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1452	847	2299
ExAC	4149	2472	6621

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.501	0.113
	0.523	0.108
(flanking)	2.053	0.111

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 marginally increased	16770	wt: 0.8820 / mu: 0.8920 (marginal change - not scored)	wt: CTGAGAGGAGACTAA mu: CTGAGAGGGGACTAA	GAGA\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

352

mutated

not conserved

352

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000006235

123

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029097

308

Ggallus

not conserved

ENSGALG00000015594

270

Trubripes

not conserved

ENSTRUG00000011090

257

Drerio

not conserved

ENSDARG00000033957

250

Dmelanogaster

not conserved

FBgn0037708

213

Celegans

not conserved

C23G10.7

243

Xtropicalis

all conserved

ENSXETG00000030882

267

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2274 / 2274

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

758 / 758

position of stopcodon in wt / mu cDNA

2274 / 2274

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

2045

theoretical NMD boundary in CDS

1994

length of CDS

2274

coding sequence (CDS) position

1054

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

1054

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

16773

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

8454639

original gDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGAGACTAACTGCCAGGCAGTCC

altered gDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGGGACTAACTGCCAGGCAGTCC

original cDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGAGACTAACTGCCAGGCAGTCC

altered cDNA sequence snippet

AAGAAGAAAGGGCTGAGAGGGGACTAACTGCCAGGCAGTCC

wildtype AA sequence

MAEVGRTGIS YPGALLPQGF WAAVEVWLER PQVANKRLCG ARLEARWSAA LPCAEARGPG
TSAGSEQKER GPGPGQGSPG GGPGPRSLSG PEQGTACCEL EEAQGQCQQE EAQREAASVP
LRDSGHPGHA EGREGDFPAA DLDSLWEDFS QSLARGNSEL LAFLTSSGAG SQPEAQRELD
VVLRTVIPKT SPHCPLTTPR REIVVQDVLN GTITFLPLEE DDEGNLKVKM SNVYQIQLSH
SKEEWFISVL IFCPERWHSD GIVYPKPTWL GEELLAKLAK WSVENKKSDF KSTLSLISIM
KYSKAYQELK EKYKEMVKVW PEVTDPEKFV YEDVAIAAYL LILWEEERAE RRLTARQSFV
DLGCGNGLLV HILSSEGHPG RGIDVRRRKI WDMYGPQTQL EEDAITPNDK TLFPDVDWLI
GNHSDELTPW IPVIAARSSY NCRFFVLPCC FFDFIGRYSR RQSKKTQYRE YLDFIKEVGF
TCGFHVDEDC LRIPSTKRVC LVGKSRTYPS SREASVDEKR TQYIKSRRGC PVSPPGWELS
PSPRWVAAGS AGHCDGQQAL DARVGCVTRA WAAEHGAGPQ AEGPWLPGFH PREKAERVRN
CAALPRDFID QVVLQVANLL LGGKQLNTRS SRNGSLKTWN GGESLSLAEV ANELDTETLR
RLKRECGGLQ TLLRNSHQVF QVVNGRVHIR DWREETLWKT KQPEAKQRLL SEACKTRLCW
FFMHHPDGCA LSTDCCPFAH GPAELRPPRT TPRKKIS*

mutated AA sequence

MAEVGRTGIS YPGALLPQGF WAAVEVWLER PQVANKRLCG ARLEARWSAA LPCAEARGPG
TSAGSEQKER GPGPGQGSPG GGPGPRSLSG PEQGTACCEL EEAQGQCQQE EAQREAASVP
LRDSGHPGHA EGREGDFPAA DLDSLWEDFS QSLARGNSEL LAFLTSSGAG SQPEAQRELD
VVLRTVIPKT SPHCPLTTPR REIVVQDVLN GTITFLPLEE DDEGNLKVKM SNVYQIQLSH
SKEEWFISVL IFCPERWHSD GIVYPKPTWL GEELLAKLAK WSVENKKSDF KSTLSLISIM
KYSKAYQELK EKYKEMVKVW PEVTDPEKFV YEDVAIAAYL LILWEEERAE RGLTARQSFV
DLGCGNGLLV HILSSEGHPG RGIDVRRRKI WDMYGPQTQL EEDAITPNDK TLFPDVDWLI
GNHSDELTPW IPVIAARSSY NCRFFVLPCC FFDFIGRYSR RQSKKTQYRE YLDFIKEVGF
TCGFHVDEDC LRIPSTKRVC LVGKSRTYPS SREASVDEKR TQYIKSRRGC PVSPPGWELS
PSPRWVAAGS AGHCDGQQAL DARVGCVTRA WAAEHGAGPQ AEGPWLPGFH PREKAERVRN
CAALPRDFID QVVLQVANLL LGGKQLNTRS SRNGSLKTWN GGESLSLAEV ANELDTETLR
RLKRECGGLQ TLLRNSHQVF QVVNGRVHIR DWREETLWKT KQPEAKQRLL SEACKTRLCW
FFMHHPDGCA LSTDCCPFAH GPAELRPPRT TPRKKIS*

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems