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: ENST00000399002
Querying Taster for transcript #2: ENST00000378194
MT speed 0 s - this script 2.684618 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPTLC3	polymorphism_automatic	0.000519969017343969	simple_aae		affected		L140V	single base exchange	rs243887		show file
SPTLC3	polymorphism_automatic	0.000519969017343969	simple_aae		affected		L140V	single base exchange	rs243887		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999480030982656 (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)

chr20:13053018T>GN/A show variant in all transcripts IGV

HGNC symbol

SPTLC3

Ensembl transcript ID

ENST00000399002

Genbank transcript ID

NM_018327

UniProt peptide

Q9NUV7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.418T>G
cDNA.692T>G
g.63392T>G

AA changes

L140V Score: 32 explain score(s)

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

140

frameshift

known variant

Reference ID: rs243887

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1421	844	2265
ExAC	31391	-30015	1376

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.413	0.002
	-0.671	0.001
(flanking)	5.021	0.596

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
Acc marginally increased	63393	wt: 0.3799 / mu: 0.3811 (marginal change - not scored)	wt: CCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGACG mu: CCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGACG	attt\|GATG
Donor gained	63391	0.99	mu: TTTGATGTGATGGAG	TGAT\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

140

mutated

all conserved

140

Ptroglodytes

all conserved

ENSPTRG00000013255

140

Mmulatta

all conserved

ENSMMUG00000000089

102

Fcatus

no alignment

ENSFCAG00000014296

n/a

Mmusculus

all conserved

ENSMUSG00000039092

140

Ggallus

all identical

ENSGALG00000009037

104

Trubripes

all identical

ENSTRUG00000000176

130

Drerio

all identical

ENSDARG00000030743

141

Dmelanogaster

all identical

FBgn0002524

194

Celegans

all identical

F43H9.2

182

Xtropicalis

all identical

ENSXETG00000008083

103

protein features

start (aa)	end (aa)	feature	details
371	371	MOD_RES	N6-(pyridoxal phosphate)lysine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1659 / 1659

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

553 / 553

position of stopcodon in wt / mu cDNA

1933 / 1933

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

275 / 275

chromosome

strand

last intron/exon boundary

1820

theoretical NMD boundary in CDS

1495

length of CDS

1659

coding sequence (CDS) position

418

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

692

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

63392

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

13053018

original gDNA sequence snippet

CCCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGAC

altered gDNA sequence snippet

CCCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGAC

original cDNA sequence snippet

CCCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGAC

altered cDNA sequence snippet

CCCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGAC

wildtype AA sequence

MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL IVESFEEAPL
HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ KDFVPLYQDF ENFYTRNLYM
RIRDNWNRPI CSAPGPLFDL MERVSDDYNW TFRFTGRVIK DVINMGSYNF LGLAAKYDES
MRTIKDVLEV YGTGVASTRH EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA
LVGKGCLILS DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG VTEFFGLDPH
EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA SSMSPPIAEQ IIRSLKLIMG
LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF IIYGNENASV VPLLLYMPGK VAAFARHMLE
KKIGVVVVGF PATPLAEARA RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP
ELYDETSFEL ED*

mutated AA sequence

MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL IVESFEEAPL
HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ KDFVPLYQDF ENFYTRNLYM
RIRDNWNRPI CSAPGPLFDV MERVSDDYNW TFRFTGRVIK DVINMGSYNF LGLAAKYDES
MRTIKDVLEV YGTGVASTRH EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA
LVGKGCLILS DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG VTEFFGLDPH
EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA SSMSPPIAEQ IIRSLKLIMG
LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF IIYGNENASV VPLLLYMPGK VAAFARHMLE
KKIGVVVVGF PATPLAEARA RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP
ELYDETSFEL ED*

speed

0.53 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: 0.999480030982656 (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)

chr20:13053018T>GN/A show variant in all transcripts IGV

HGNC symbol

SPTLC3

Ensembl transcript ID

ENST00000378194

Genbank transcript ID

N/A

UniProt peptide

Q9NUV7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.418T>G
cDNA.512T>G
g.63392T>G

AA changes

L140V Score: 32 explain score(s)

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

140

frameshift

known variant

Reference ID: rs243887

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1421	844	2265
ExAC	31391	-30015	1376

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.413	0.002
	-0.671	0.001
(flanking)	5.021	0.596

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
Acc marginally increased	63393	wt: 0.3799 / mu: 0.3811 (marginal change - not scored)	wt: CCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGACG mu: CCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGACG	attt\|GATG
Donor gained	63391	0.99	mu: TTTGATGTGATGGAG	TGAT\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

140

mutated

all conserved

140

Ptroglodytes

all conserved

ENSPTRG00000013255

140

Mmulatta

all conserved

ENSMMUG00000000089

102

Fcatus

no alignment

ENSFCAG00000014296

n/a

Mmusculus

all conserved

ENSMUSG00000039092

140

Ggallus

all identical

ENSGALG00000009037

104

Trubripes

all identical

ENSTRUG00000000176

130

Drerio

all identical

ENSDARG00000030743

141

Dmelanogaster

all identical

FBgn0002524

194

Celegans

all identical

F43H9.2

182

Xtropicalis

all identical

ENSXETG00000008083

103

protein features

start (aa)	end (aa)	feature	details
371	371	MOD_RES	N6-(pyridoxal phosphate)lysine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

990 / 990

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

330 / 330

position of stopcodon in wt / mu cDNA

1084 / 1084

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

95 / 95

chromosome

strand

last intron/exon boundary

1290

theoretical NMD boundary in CDS

1145

length of CDS

990

coding sequence (CDS) position

418

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

512

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

63392

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

13053018

original gDNA sequence snippet

CCCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGAC

altered gDNA sequence snippet

CCCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGAC

original cDNA sequence snippet

CCCCAGGGCCTCTGTTTGATTTGATGGAGAGGGTATCAGAC

altered cDNA sequence snippet

CCCCAGGGCCTCTGTTTGATGTGATGGAGAGGGTATCAGAC

wildtype AA sequence

mutated AA sequence

speed

0.60 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems