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: ENST00000013222
Querying Taster for transcript #2: ENST00000409539
MT speed 0 s - this script 3.533753 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
INMT	polymorphism_automatic	0.00113330126626499	simple_aae				F254C	single base exchange	rs4720015		show file
INMT	polymorphism_automatic	0.00113330126626499	simple_aae				F253C	single base exchange	rs4720015		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998866698733735 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM097282)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:30795436T>GN/A show variant in all transcripts IGV

HGNC symbol

INMT

Ensembl transcript ID

ENST00000013222

Genbank transcript ID

NM_006774

UniProt peptide

O95050

alteration type

single base exchange

alteration region

CDS

DNA changes

c.761T>G
cDNA.777T>G
g.57836T>G

AA changes

F254C Score: 205 explain score(s)

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

254

frameshift

known variant

Reference ID: rs4720015

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1563	746	2309
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM097282)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.863	0.445
	0.721	0.409
(flanking)	0.414	0.322

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

399

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

254

mutated

not conserved

254

Ptroglodytes

all identical

ENSPTRG00000019045

254

Mmulatta

all identical

ENSMMUG00000011760

254

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086998

254

Dmelanogaster

no homologue

Celegans

not conserved

T07C12.9

280

Xtropicalis

no alignment

ENSXETG00000008551

n/a

protein features

start (aa)	end (aa)	feature	details
252	259	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

792 / 792

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

264 / 264

position of stopcodon in wt / mu cDNA

808 / 808

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

17 / 17

chromosome

strand

last intron/exon boundary

379

theoretical NMD boundary in CDS

312

length of CDS

792

coding sequence (CDS) position

761

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

777

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

57836

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

30795436

original gDNA sequence snippet

TGCCAACAATGGGGTCTGCTTCATTGTGGCTCGCAAGAAGC

altered gDNA sequence snippet

TGCCAACAATGGGGTCTGCTGCATTGTGGCTCGCAAGAAGC

original cDNA sequence snippet

TGCCAACAATGGGGTCTGCTTCATTGTGGCTCGCAAGAAGC

altered cDNA sequence snippet

TGCCAACAATGGGGTCTGCTGCATTGTGGCTCGCAAGAAGC

wildtype AA sequence

MKGGFTGGDE YQKHFLPRDY LATYYSFDGS PSPEAEMLKF NLECLHKTFG PGGLQGDTLI
DIGSGPTIYQ VLAACDSFQD ITLSDFTDRN REELEKWLKK EPGAYDWTPA VKFACELEGN
SGRWEEKEEK LRAAVKRVLK CDVHLGNPLA PAVLPLADCV LTLLAMECAC CSLDAYRAAL
CNLASLLKPG GHLVTTVTLR LPSYMVGKRE FSCVALEKEE VEQAVLDAGF DIEQLLHSPQ
SYSVTNAANN GVCFIVARKK PGP*

mutated AA sequence

speed

0.80 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: 0.998866698733735 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM097282)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:30795436T>GN/A show variant in all transcripts IGV

HGNC symbol

INMT

Ensembl transcript ID

ENST00000409539

Genbank transcript ID

NM_001199219

UniProt peptide

O95050

alteration type

single base exchange

alteration region

CDS

DNA changes

c.758T>G
cDNA.772T>G
g.57836T>G

AA changes

F253C Score: 205 explain score(s)

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

253

frameshift

known variant

Reference ID: rs4720015

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1563	746	2309
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM097282)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.863	0.445
	0.721	0.409
(flanking)	0.414	0.322

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

253

mutated

not conserved

253

Ptroglodytes

all identical

ENSPTRG00000019045

254

Mmulatta

all identical

ENSMMUG00000011760

254

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086998

254

Dmelanogaster

no homologue

Celegans

not conserved

T07C12.9

280

Xtropicalis

no alignment

ENSXETG00000008551

n/a

protein features

start (aa)	end (aa)	feature	details
252	259	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

789 / 789

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

263 / 263

position of stopcodon in wt / mu cDNA

803 / 803

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

15 / 15

chromosome

strand

last intron/exon boundary

374

theoretical NMD boundary in CDS

309

length of CDS

789

coding sequence (CDS) position

758

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

772

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

57836

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

30795436

original gDNA sequence snippet

TGCCAACAATGGGGTCTGCTTCATTGTGGCTCGCAAGAAGC

altered gDNA sequence snippet

TGCCAACAATGGGGTCTGCTGCATTGTGGCTCGCAAGAAGC

original cDNA sequence snippet

TGCCAACAATGGGGTCTGCTTCATTGTGGCTCGCAAGAAGC

altered cDNA sequence snippet

TGCCAACAATGGGGTCTGCTGCATTGTGGCTCGCAAGAAGC

wildtype AA sequence

MKGGFTGGDE YQKHFLPRDY LATYYSFDGS PSPEAEMLKF NLECLHKTFG PGLQGDTLID
IGSGPTIYQV LAACDSFQDI TLSDFTDRNR EELEKWLKKE PGAYDWTPAV KFACELEGNS
GRWEEKEEKL RAAVKRVLKC DVHLGNPLAP AVLPLADCVL TLLAMECACC SLDAYRAALC
NLASLLKPGG HLVTTVTLRL PSYMVGKREF SCVALEKEEV EQAVLDAGFD IEQLLHSPQS
YSVTNAANNG VCFIVARKKP GP*

mutated AA sequence

speed

0.74 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems