MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000340951
Querying Taster for transcript #2: ENST00000479452
Querying Taster for transcript #3: ENST00000342129
MT speed 0 s - this script 3.603134 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EXD3	polymorphism_automatic	1.15141696177545e-09	simple_aae		affected		A160T	single base exchange	rs11533158		show file
EXD3	polymorphism_automatic	1.15141696177545e-09	simple_aae		affected		A160T	single base exchange	rs11533158		show file
EXD3	polymorphism_automatic	0.00191247034293696	without_aae		affected			single base exchange	rs11533158		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999998848583 (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)

chr9:140262426C>TN/A show variant in all transcripts IGV

HGNC symbol

EXD3

Ensembl transcript ID

ENST00000340951

Genbank transcript ID

NM_017820

UniProt peptide

Q8N9H8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.478G>A
cDNA.674G>A
g.55289G>A

AA changes

A160T Score: 58 explain score(s)

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

160

frameshift

known variant

Reference ID: rs11533158

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1293	950	2243
ExAC	29158	-25549	3609

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.211	0.211
	-0.239	0.211
(flanking)	1.873	0.257

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 marginally increased	55294	wt: 0.9405 / mu: 0.9766 (marginal change - not scored)	wt: GCGACGTTGAAGCTG mu: ACGACGTTGAAGCTG	GACG\|ttga
Donor increased	55281	wt: 0.55 / mu: 0.78	wt: AGCCACGCTGGGCGC mu: AGCCACGCTGGGCAC	CCAC\|gctg
Donor gained	55285	0.81	mu: ACGCTGGGCACGACG	GCTG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

160

mutated

not conserved

160

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000032154

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000063140

152

Dmelanogaster

not conserved

FBgn0032924

194

Celegans

not conserved

ZK1098.3

187

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
160	160	CONFLICT	A -> T (in Ref. 2; BAC04356 and 4; AAH37355/AAI10880).	lost
249	249	CONFLICT	G -> S (in Ref. 2; BAC04356).	might get lost (downstream of altered splice site)
322	322	CONFLICT	E -> D (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)
517	571	DOMAIN	3'-5' exonuclease.	might get lost (downstream of altered splice site)
519	519	CONFLICT	S -> T (in Ref. 1; BAC10986).	might get lost (downstream of altered splice site)
545	545	CONFLICT	C -> Y (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2631 / 2631

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

877 / 877

position of stopcodon in wt / mu cDNA

2827 / 2827

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

197 / 197

chromosome

strand

-1

last intron/exon boundary

2514

theoretical NMD boundary in CDS

2267

length of CDS

2631

coding sequence (CDS) position

478

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

674

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

55289

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

140262426

original gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

original cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

wildtype AA sequence

MDPGDPAGDP AAGERHRMGR DPLLLLQALQ TLWSTRERKQ LREEAWRGFA ALDDPLAGLL
DMLESCRGQR GEGPSLAAWI SHQLQCWLQA QPCPSLAQHS LRLKQLQARA VKVLTESPPS
LAAPLASIFQ LQDADRSCLL AHVHRLHHEG RFREAATLGA TLKLQSELGV EKMSIPLLLQ
DKVALVERYV AGFPDLQRRL LVLMDSWCQP GFDIKDVARR YPEVTSLSLE KLSPKALSRQ
VLRLQERYGV APALCPNAAI QQRLAALRHL CHKRFVEKSL SQENWTDHVQ GLVGQSPWLQ
EQLSQLLVSH SDPVTAAQCA MELLLPEERL PAAVAVELRR FRLQGRATEA DSRLEVKDMK
DRYYQLPIPR ENVHLLASWE DLTRHEGALL QCHQVVGVDV EWTPVFVAGG RPRPSLLQVA
VEGHVFLLDV LALSQPPTGQ GAQAFSRLVA QLLSDPSITK LGYGMVGDLQ KLGTSCPALA
HVEKQILGGM DLLLVHRQMR VASVPAPAVD RARELRGLSL LVQQVLGTAL DKTQQLSNWD
RRPLCEEQVI YAAADAYCLL EVHQALCREP ARFHLSEDLA GSRRPRHRER PGARKPPGLQ
KASAPAAPRQ VPVAVAVSEG AAPQIPARAF RVVCDNMLQG LARSLRCLGV DARMLGNGED
HRRAAEVARQ EGRIILTSGQ PFHKLRAQVG AGRCLSVDCS LKAQQQAKAV LKHFNVRVTH
ADIFSRCQAC NCDQYLKVSR DMMKQLMWLS SHQEGPRSSG DEATQSQAVQ EPGPAPDAAP
EGCTYDRPCR WLQMADLRAE TPDMLADGTR LQLAGVPVGV LRTPGLRCFY CCTGCGKVFW
DGSHLGRVAT HFRDMLESAP SPCEPSPAPS PASSPF*

mutated AA sequence

MDPGDPAGDP AAGERHRMGR DPLLLLQALQ TLWSTRERKQ LREEAWRGFA ALDDPLAGLL
DMLESCRGQR GEGPSLAAWI SHQLQCWLQA QPCPSLAQHS LRLKQLQARA VKVLTESPPS
LAAPLASIFQ LQDADRSCLL AHVHRLHHEG RFREAATLGT TLKLQSELGV EKMSIPLLLQ
DKVALVERYV AGFPDLQRRL LVLMDSWCQP GFDIKDVARR YPEVTSLSLE KLSPKALSRQ
VLRLQERYGV APALCPNAAI QQRLAALRHL CHKRFVEKSL SQENWTDHVQ GLVGQSPWLQ
EQLSQLLVSH SDPVTAAQCA MELLLPEERL PAAVAVELRR FRLQGRATEA DSRLEVKDMK
DRYYQLPIPR ENVHLLASWE DLTRHEGALL QCHQVVGVDV EWTPVFVAGG RPRPSLLQVA
VEGHVFLLDV LALSQPPTGQ GAQAFSRLVA QLLSDPSITK LGYGMVGDLQ KLGTSCPALA
HVEKQILGGM DLLLVHRQMR VASVPAPAVD RARELRGLSL LVQQVLGTAL DKTQQLSNWD
RRPLCEEQVI YAAADAYCLL EVHQALCREP ARFHLSEDLA GSRRPRHRER PGARKPPGLQ
KASAPAAPRQ VPVAVAVSEG AAPQIPARAF RVVCDNMLQG LARSLRCLGV DARMLGNGED
HRRAAEVARQ EGRIILTSGQ PFHKLRAQVG AGRCLSVDCS LKAQQQAKAV LKHFNVRVTH
ADIFSRCQAC NCDQYLKVSR DMMKQLMWLS SHQEGPRSSG DEATQSQAVQ EPGPAPDAAP
EGCTYDRPCR WLQMADLRAE TPDMLADGTR LQLAGVPVGV LRTPGLRCFY CCTGCGKVFW
DGSHLGRVAT HFRDMLESAP SPCEPSPAPS PASSPF*

speed

0.78 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: 0.999999998848583 (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)

chr9:140262426C>TN/A show variant in all transcripts IGV

HGNC symbol

EXD3

Ensembl transcript ID

ENST00000479452

Genbank transcript ID

N/A

UniProt peptide

Q8N9H8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.478G>A
cDNA.567G>A
g.55289G>A

AA changes

A160T Score: 58 explain score(s)

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

160

frameshift

known variant

Reference ID: rs11533158

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1293	950	2243
ExAC	29158	-25549	3609

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.211	0.211
	-0.239	0.211
(flanking)	1.873	0.257

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 marginally increased	55294	wt: 0.9405 / mu: 0.9766 (marginal change - not scored)	wt: GCGACGTTGAAGCTG mu: ACGACGTTGAAGCTG	GACG\|ttga
Donor increased	55281	wt: 0.55 / mu: 0.78	wt: AGCCACGCTGGGCGC mu: AGCCACGCTGGGCAC	CCAC\|gctg
Donor gained	55285	0.81	mu: ACGCTGGGCACGACG	GCTG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

160

mutated

not conserved

160

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000032154

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000063140

152

Dmelanogaster

not conserved

FBgn0032924

194

Celegans

not conserved

ZK1098.3

187

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
160	160	CONFLICT	A -> T (in Ref. 2; BAC04356 and 4; AAH37355/AAI10880).	lost
249	249	CONFLICT	G -> S (in Ref. 2; BAC04356).	might get lost (downstream of altered splice site)
322	322	CONFLICT	E -> D (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)
517	571	DOMAIN	3'-5' exonuclease.	might get lost (downstream of altered splice site)
519	519	CONFLICT	S -> T (in Ref. 1; BAC10986).	might get lost (downstream of altered splice site)
545	545	CONFLICT	C -> Y (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

741 / 741

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

247 / 247

position of stopcodon in wt / mu cDNA

830 / 830

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

90 / 90

chromosome

strand

-1

last intron/exon boundary

746

theoretical NMD boundary in CDS

606

length of CDS

741

coding sequence (CDS) position

478

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

567

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

55289

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

140262426

original gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

original cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

wildtype AA sequence

mutated AA sequence

speed

0.84 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.998087529657063 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr9:140262426C>TN/A show variant in all transcripts IGV

HGNC symbol

EXD3

Ensembl transcript ID

ENST00000342129

Genbank transcript ID

N/A

UniProt peptide

Q8N9H8

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.674G>A
g.55289G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11533158

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1293	950	2243
ExAC	29158	-25549	3609

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.211	0.211
	-0.239	0.211
(flanking)	1.873	0.257

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

splice sites

splice site change before start ATG (at aa -162) | splice site change before start ATG (at aa -161) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	55294	wt: 0.9405 / mu: 0.9766 (marginal change - not scored)	wt: GCGACGTTGAAGCTG mu: ACGACGTTGAAGCTG	GACG\|ttga
Donor increased	55281	wt: 0.55 / mu: 0.78	wt: AGCCACGCTGGGCGC mu: AGCCACGCTGGGCAC	CCAC\|gctg
Donor gained	55285	0.81	mu: ACGCTGGGCACGACG	GCTG\|ggca

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
105	105	CONFLICT	Q -> R (in Ref. 1; BAC10986 and 2; BAB70838/BAC04356).	might get lost (downstream of altered splice site)
160	160	CONFLICT	A -> T (in Ref. 2; BAC04356 and 4; AAH37355/AAI10880).	might get lost (downstream of altered splice site)
249	249	CONFLICT	G -> S (in Ref. 2; BAC04356).	might get lost (downstream of altered splice site)
322	322	CONFLICT	E -> D (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)
517	571	DOMAIN	3'-5' exonuclease.	might get lost (downstream of altered splice site)
519	519	CONFLICT	S -> T (in Ref. 1; BAC10986).	might get lost (downstream of altered splice site)
545	545	CONFLICT	C -> Y (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)

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

1157 / 1157

chromosome

strand

-1

last intron/exon boundary

2388

theoretical NMD boundary in CDS

1181

length of CDS

1545

coding sequence (CDS) position

N/A

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

674

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

55289

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

140262426

original gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

original cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

wildtype AA sequence

MELLLPEERL PAAVAVELRR FRLQGRATEA DSRLEVKDMK DRYYQLPIPR ENVHLLASWE
DLTRHEGALL QCHQVVGVDV EWTPVFVAGG RPRPSLLQVA VEGHVFLLDV LALSQPPTGQ
GAQAFSRLVA QLLSDPSITK LGYGMVGDLQ KLGTSCPALA HVEKQILGGM DLLLVHRQMR
VASVPAPAVD RARELRGLSL LVQQVLGTAL DKTQQLSNWD RRPLCEEQVI YAAADAYCLL
EVHQALCREP ARFHLSEDLA GSRRPRHRER PGARKPPGLQ KASAPAAPRQ GLARSLRCLG
VDARMLGNGE DHRRAAEVAR QEGRIILTSG QPFHKLRAQV GAGRCLSVDC SLKAQQQAKA
VLKHFNVRVT HADIFSRCQA CNCDQYLKVS RDMMKQLMWL SSHQEGPRSS GPAPDAAPEG
CTYDRPCRWL QMADLRAETP DMLADGTRLQ LAGVPVGVLR TPGLRCFYCC TGCGKVFWDG
SHLGRVATHF RDMLESAPSP CEPSPAPSPA SSPF*

mutated AA sequence

N/A

speed

0.73 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems