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: ENST00000319540
Querying Taster for transcript #2: ENST00000273908
MT speed 0 s - this script 3.266632 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SCD5	polymorphism_automatic	9.20374887414255e-14	simple_aae				L246M	single base exchange	rs3733228		show file
SCD5	polymorphism_automatic	0.988106760351707	without_aae					single base exchange	rs3733228		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999908 (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)

chr4:83582064G>TN/A show variant in all transcripts IGV

HGNC symbol

SCD5

Ensembl transcript ID

ENST00000273908

Genbank transcript ID

NM_024906

UniProt peptide

Q86SK9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.736C>A
cDNA.971C>A
g.137947C>A

AA changes

L246M Score: 15 explain score(s)

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

246

frameshift

known variant

Reference ID: rs3733228

database	homozygous (T/T)	heterozygous	allele carriers
1000G	285	946	1231
ExAC	7364	18039	25403

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.258	0
	2.481	0.005
(flanking)	-0.521	0

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

167

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

246

mutated

all conserved

246

Ptroglodytes

no alignment

ENSPTRG00000016220

n/a

Mmulatta

no alignment

ENSMMUG00000000866

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000011173

n/a

Trubripes

no alignment

ENSTRUG00000012356

n/a

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0086687

n/a

Celegans

no alignment

W06D12.3

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

771 / 771

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

257 / 257

position of stopcodon in wt / mu cDNA

1006 / 1006

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

236 / 236

chromosome

strand

-1

last intron/exon boundary

805

theoretical NMD boundary in CDS

519

length of CDS

771

coding sequence (CDS) position

736

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

971

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

137947

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

83582064

original gDNA sequence snippet

CCGAAAAGTGCTGCTTGATGCTGCGTGCTCTTTCTGTGTCC

altered gDNA sequence snippet

CCGAAAAGTGCTGCTTGATGATGCGTGCTCTTTCTGTGTCC

original cDNA sequence snippet

CCGAAAAGTGCTGCTTGATGCTGCGTGCTCTTTCTGTGTCC

altered cDNA sequence snippet

CCGAAAAGTGCTGCTTGATGATGCGTGCTCTTTCTGTGTCC

wildtype AA sequence

MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRN TQHIQKEGRA LNQEAACEML REWHQGHILK VTLPGLHILA LLHTHCNHSE
KCCLMLRALS VSLEVF*

mutated AA sequence

speed

0.71 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: without_aae, prob: 0.0118932396482927 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:83582064G>TN/A show variant in all transcripts IGV

HGNC symbol

SCD5

Ensembl transcript ID

ENST00000319540

Genbank transcript ID

NM_001037582

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.137947C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3733228

database	homozygous (T/T)	heterozygous	allele carriers
1000G	285	946	1231
ExAC	7364	18039	25403

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.258	0
	2.481	0.005
(flanking)	-0.521	0

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

19796

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

321 / 321

chromosome

strand

-1

last intron/exon boundary

1123

theoretical NMD boundary in CDS

752

length of CDS

993

coding sequence (CDS) position

N/A

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

N/A

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

137947

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

83582064

original gDNA sequence snippet

CCGAAAAGTGCTGCTTGATGCTGCGTGCTCTTTCTGTGTCC

altered gDNA sequence snippet

CCGAAAAGTGCTGCTTGATGATGCGTGCTCTTTCTGTGTCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRK YYKISVVLMC FVVPTLVPWY IWGESLWNSY FLASILRYTI SLNISWLVNS
AAHMYGNRPY DKHISPRQNP LVALGAIGEG FHNYHHTFPF DYSASEFGLN FNPTTWFIDF
MCWLGLATDR KRATKPMIEA RKARTGDSSA *

mutated AA sequence

N/A

speed

0.61 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems