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: ENST00000305560
Querying Taster for transcript #2: ENST00000559860
MT speed 0 s - this script 2.688584 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPATA5L1	polymorphism_automatic	9.99200722162641e-15	simple_aae		affected		R119P	single base exchange	rs1153850		show file
SPATA5L1	polymorphism_automatic	9.99200722162641e-15	simple_aae		affected		R119P	single base exchange	rs1153850		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999999 (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)

chr15:45694983G>CN/A show variant in all transcripts IGV

HGNC symbol

SPATA5L1

Ensembl transcript ID

ENST00000559860

Genbank transcript ID

N/A

UniProt peptide

Q9BVQ7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.356G>C
cDNA.416G>C
g.455G>C

AA changes

R119P Score: 103 explain score(s)

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

119

frameshift

known variant

Reference ID: rs1153850

database	homozygous (C/C)	heterozygous	allele carriers
1000G	196	412	608
ExAC	610	2153	2763

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Ini1, Transcription Factor, Ini1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.027	0
	-2.6	0
(flanking)	-0.18	0

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 increased	459	wt: 0.81 / mu: 0.92	wt: CGGGCAGGCGCGCCC mu: CCGGCAGGCGCGCCC	GGCA\|ggcg
Donor increased	455	wt: 0.69 / mu: 0.89	wt: AGAGCGGGCAGGCGC mu: AGAGCCGGCAGGCGC	AGCG\|ggca

distance from splice site

416

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

119

mutated

not conserved

119

Ptroglodytes

all conserved

ENSPTRG00000007034

Mmulatta

not conserved

ENSMMUG00000005858

119

Fcatus

no alignment

ENSFCAG00000019110

n/a

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000005682

117

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000061763

108

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
241	248	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
257	257	CONFLICT	E -> G (in Ref. 1; BAB14017).	might get lost (downstream of altered splice site)
505	512	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1863 / 1863

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

621 / 621

position of stopcodon in wt / mu cDNA

1923 / 1923

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

61 / 61

chromosome

strand

last intron/exon boundary

1705

theoretical NMD boundary in CDS

1594

length of CDS

1863

coding sequence (CDS) position

356

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

416

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

455

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

45694983

original gDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCGGGCAGGCGCGCCCGGTGCCC

altered gDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCCGGCAGGCGCGCCCGGTGCCC

original cDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCGGGCAGGCGCGCCCGGTGCCC

altered cDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCCGGCAGGCGCGCCCGGTGCCC

wildtype AA sequence

MAPDSDPFPE GPLLKLLPLD ARDRGTQRCR LGPAALHALG ARLGSAVKIS LPDGGSCLCT
AWPRRDGADG FVQLDPLCAS PGAAVGASRS RRSLSLNRLL LVPCPPLRRV AVWPVLRERA
GAPGARNTAA VLEAAQELLR NRPISLGHVV VAPPGAPGLV AALHIVGGTP SPDPAGLVTP
RTRVSLGGEP PSEAQPQPEV PLGGLSEAAD SLRELLRLPL RYPRALTALG LAVPRGVLLA
GPPGVGKTQL VRAVAREAGA ELLAVSAPAL QGSRPGETEE NVRRVFQRAR ELASRGPSLL
FLDEMDALCP QRGSRAPESR VVAQVLTLLD GASGDREVVV VGATNRPDAL DPALRRPGRF
DREVVIGTPT LKQRKEILQV ITSKMPISSH VDLGLLAEMT VGYVGADLTA LCREAAMHAL
LHSEKNQDNP VIDEIDFLEA FKNIQPSSFR SVIGLMDIKP VDWEEIGGLE DVKLKLKQSI
EWPLKFPWEF VRMGLTQPKG VLLYGPPGCA KTTLVRALAT SCHCSFVSVS GADLFSPFVG
DSEKVLSQIF RQARASTPAI LFLDEIDSIL GARSASKTGC DVQERVLSVL LNELDGVGLK
TIERRGSKSS QQGKYKELKK *

mutated AA sequence

MAPDSDPFPE GPLLKLLPLD ARDRGTQRCR LGPAALHALG ARLGSAVKIS LPDGGSCLCT
AWPRRDGADG FVQLDPLCAS PGAAVGASRS RRSLSLNRLL LVPCPPLRRV AVWPVLREPA
GAPGARNTAA VLEAAQELLR NRPISLGHVV VAPPGAPGLV AALHIVGGTP SPDPAGLVTP
RTRVSLGGEP PSEAQPQPEV PLGGLSEAAD SLRELLRLPL RYPRALTALG LAVPRGVLLA
GPPGVGKTQL VRAVAREAGA ELLAVSAPAL QGSRPGETEE NVRRVFQRAR ELASRGPSLL
FLDEMDALCP QRGSRAPESR VVAQVLTLLD GASGDREVVV VGATNRPDAL DPALRRPGRF
DREVVIGTPT LKQRKEILQV ITSKMPISSH VDLGLLAEMT VGYVGADLTA LCREAAMHAL
LHSEKNQDNP VIDEIDFLEA FKNIQPSSFR SVIGLMDIKP VDWEEIGGLE DVKLKLKQSI
EWPLKFPWEF VRMGLTQPKG VLLYGPPGCA KTTLVRALAT SCHCSFVSVS GADLFSPFVG
DSEKVLSQIF RQARASTPAI LFLDEIDSIL GARSASKTGC DVQERVLSVL LNELDGVGLK
TIERRGSKSS QQGKYKELKK *

speed

0.55 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: 0.99999999999999 (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)

chr15:45694983G>CN/A show variant in all transcripts IGV

HGNC symbol

SPATA5L1

Ensembl transcript ID

ENST00000305560

Genbank transcript ID

NM_024063

UniProt peptide

Q9BVQ7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.356G>C
cDNA.455G>C
g.455G>C

AA changes

R119P Score: 103 explain score(s)

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

119

frameshift

known variant

Reference ID: rs1153850

database	homozygous (C/C)	heterozygous	allele carriers
1000G	196	412	608
ExAC	610	2153	2763

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.027	0
	-2.6	0
(flanking)	-0.18	0

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 increased	459	wt: 0.81 / mu: 0.92	wt: CGGGCAGGCGCGCCC mu: CCGGCAGGCGCGCCC	GGCA\|ggcg
Donor increased	455	wt: 0.69 / mu: 0.89	wt: AGAGCGGGCAGGCGC mu: AGAGCCGGCAGGCGC	AGCG\|ggca

distance from splice site

455

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

119

mutated

not conserved

119

Ptroglodytes

all conserved

ENSPTRG00000007034

Mmulatta

not conserved

ENSMMUG00000005858

119

Fcatus

no alignment

ENSFCAG00000019110

n/a

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000005682

117

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000061763

108

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
241	248	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
257	257	CONFLICT	E -> G (in Ref. 1; BAB14017).	might get lost (downstream of altered splice site)
505	512	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2262 / 2262

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

754 / 754

position of stopcodon in wt / mu cDNA

2361 / 2361

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

100 / 100

chromosome

strand

last intron/exon boundary

2194

theoretical NMD boundary in CDS

2044

length of CDS

2262

coding sequence (CDS) position

356

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

455

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

455

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

45694983

original gDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCGGGCAGGCGCGCCCGGTGCCC

altered gDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCCGGCAGGCGCGCCCGGTGCCC

original cDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCGGGCAGGCGCGCCCGGTGCCC

altered cDNA sequence snippet

GTGGCCGGTGTTGCGAGAGCCGGCAGGCGCGCCCGGTGCCC

wildtype AA sequence

mutated AA sequence

speed

0.57 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems