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: ENST00000588525
Querying Taster for transcript #2: ENST00000252675
MT speed 0 s - this script 3.35385 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FUT5	polymorphism_automatic	5.50488874969668e-05	simple_aae				T338M	single base exchange	rs4807054		show file
FUT5	polymorphism_automatic	5.50488874969668e-05	simple_aae				T338M	single base exchange	rs4807054		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999944951112503 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:5866724G>AN/A show variant in all transcripts IGV

HGNC symbol

FUT5

Ensembl transcript ID

ENST00000588525

Genbank transcript ID

NM_002034

UniProt peptide

Q11128

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1013C>T
cDNA.1101C>T
g.37075C>T

AA changes

T338M Score: 81 explain score(s)

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

338

frameshift

known variant

Reference ID: rs4807054

database	homozygous (A/A)	heterozygous	allele carriers
1000G	451	1102	1553
ExAC	9927	12913	22840

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0.111
	1.374	0.576
(flanking)	0.423	0.646

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

888

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

338

mutated

not conserved

338

Ptroglodytes

all identical

ENSPTRG00000010347

338

Mmulatta

all identical

ENSMMUG00000028917

324

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000001806

327

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000027088

312

protein features

start (aa)	end (aa)	feature	details
35	374	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1125 / 1125

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

375 / 375

position of stopcodon in wt / mu cDNA

1213 / 1213

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

89 / 89

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

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

length of CDS

1125

coding sequence (CDS) position

1013

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

1101

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

37075

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

5866724

original gDNA sequence snippet

CTACTTTCACTGGCGGGAGACGCTGCGGCCTCGCTCCTTCA

altered gDNA sequence snippet

CTACTTTCACTGGCGGGAGATGCTGCGGCCTCGCTCCTTCA

original cDNA sequence snippet

CTACTTTCACTGGCGGGAGACGCTGCGGCCTCGCTCCTTCA

altered cDNA sequence snippet

CTACTTTCACTGGCGGGAGATGCTGCGGCCTCGCTCCTTCA

wildtype AA sequence

MDPLGPAKPQ WLWRRCLAGL LFQLLVAVCF FSYLRVSRDD ATGSPRPGLM AVEPVTGAPN
GSRCQDSMAT PAHPTLLILL WTWPFNTPVA LPRCSEMVPG AADCNITADS SVYPQADAVI
VHHWDIMYNP SANLPPPTRP QGQRWIWFSM ESPSNCRHLE ALDGYFNLTM SYRSDSDIFT
PYGWLEPWSG QPAHPPLNLS AKTELVAWAV SNWKPDSARV RYYQSLQAHL KVDVYGRSHK
PLPKGTMMET LSRYKFYLAF ENSLHPDYIT EKLWRNALEA WAVPVVLGPS RSNYERFLPP
DAFIHVDDFQ SPKDLARYLQ ELDKDHARYL SYFHWRETLR PRSFSWALAF CKACWKLQQE
SRYQTVRSIA AWFT*

mutated AA sequence

speed

0.09 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: 0.999944951112503 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:5866724G>AN/A show variant in all transcripts IGV

HGNC symbol

FUT5

Ensembl transcript ID

ENST00000252675

Genbank transcript ID

N/A

UniProt peptide

Q11128

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1013C>T
cDNA.1576C>T
g.37075C>T

AA changes

T338M Score: 81 explain score(s)

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

338

frameshift

known variant

Reference ID: rs4807054

database	homozygous (A/A)	heterozygous	allele carriers
1000G	451	1102	1553
ExAC	9927	12913	22840

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0.111
	1.374	0.576
(flanking)	0.423	0.646

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

543

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

338

mutated

not conserved

338

Ptroglodytes

all identical

ENSPTRG00000010347

338

Mmulatta

all identical

ENSMMUG00000028917

324

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000001806

327

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000027088

312

protein features

start (aa)	end (aa)	feature	details
35	374	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1125 / 1125

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

375 / 375

position of stopcodon in wt / mu cDNA

1688 / 1688

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

564 / 564

chromosome

strand

-1

last intron/exon boundary

552

theoretical NMD boundary in CDS

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

length of CDS

1125

coding sequence (CDS) position

1013

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

1576

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

37075

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

5866724

original gDNA sequence snippet

CTACTTTCACTGGCGGGAGACGCTGCGGCCTCGCTCCTTCA

altered gDNA sequence snippet

CTACTTTCACTGGCGGGAGATGCTGCGGCCTCGCTCCTTCA

original cDNA sequence snippet

CTACTTTCACTGGCGGGAGACGCTGCGGCCTCGCTCCTTCA

altered cDNA sequence snippet

CTACTTTCACTGGCGGGAGATGCTGCGGCCTCGCTCCTTCA

wildtype AA sequence

mutated AA sequence

speed

1.28 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems