MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000378364
Querying Taster for transcript #2: ENST00000426324
Querying Taster for transcript #3: ENST00000563655
MT speed 0 s - this script 4.706267 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APRT	disease_causing_automatic	0.999999572344634	simple_aae		affected	0	M109T	single base exchange	rs28999113		show file
APRT	disease_causing_automatic	0.999999682191211	simple_aae		affected	0	M136T	single base exchange	rs28999113		show file
APRT	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs28999113		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999572344634 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM880009)
known disease mutation: rs18296 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88876242A>GN/A show variant in all transcripts IGV

HGNC symbol

APRT

Ensembl transcript ID

ENST00000563655

Genbank transcript ID

N/A

UniProt peptide

P07741

alteration type

single base exchange

alteration region

CDS

DNA changes

c.326T>C
cDNA.347T>C
g.2111T>C

AA changes

M109T Score: 81 explain score(s)

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

109

frameshift

known variant

Reference ID: rs28999113
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18296 (pathogenic for Adenine phosphoribosyltransferase deficiency|APRT deficiency, Japanese type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.269	1
	4.364	1
(flanking)	2.822	1

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	2105	wt: 0.2583 / mu: 0.3307 (marginal change - not scored)	wt: CCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGTG mu: CCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGTG	cagg\|AACC
Acc marginally increased	2104	wt: 0.8036 / mu: 0.8236 (marginal change - not scored)	wt: ACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGT mu: ACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGT	ccag\|GAAC
Acc marginally increased	2103	wt: 0.9114 / mu: 0.9248 (marginal change - not scored)	wt: GACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTG mu: GACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTG	ccca\|GGAA
Donor increased	2106	wt: 0.47 / mu: 0.70	wt: CCAGGAACCATGAAC mu: CCAGGAACCACGAAC	AGGA\|acca
Donor marginally increased	2103	wt: 0.8481 / mu: 0.8970 (marginal change - not scored)	wt: TCCCCAGGAACCATG mu: TCCCCAGGAACCACG	CCCA\|ggaa
Donor increased	2110	wt: 0.71 / mu: 0.82	wt: GAACCATGAACGCTG mu: GAACCACGAACGCTG	ACCA\|tgaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

109

mutated

not conserved

109

Ptroglodytes

all identical

ENSPTRG00000008466

136

Mmulatta

all identical

ENSMMUG00000013824

136

Fcatus

all identical

ENSFCAG00000018452

109

Mmusculus

all identical

ENSMUSG00000006589

136

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000005211

136

Drerio

all conserved

ENSDARG00000003519

134

Dmelanogaster

all conserved

FBgn0000109

140

Celegans

all conserved

T19B4.3

139

Xtropicalis

all identical

ENSXETG00000027084

136

protein features

start (aa)	end (aa)	feature	details
106	113	STRAND		lost
114	114	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
122	133	STRAND		might get lost (downstream of altered splice site)
134	145	HELIX		might get lost (downstream of altered splice site)
135	135	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
149	159	STRAND		might get lost (downstream of altered splice site)
160	162	HELIX		might get lost (downstream of altered splice site)
164	168	HELIX		might get lost (downstream of altered splice site)
173	179	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

462 / 462

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

154 / 154

position of stopcodon in wt / mu cDNA

483 / 483

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

22 / 22

chromosome

strand

-1

last intron/exon boundary

341

theoretical NMD boundary in CDS

269

length of CDS

462

coding sequence (CDS) position

326

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

347

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

2111

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

88876242

original gDNA sequence snippet

CCTCCCATCCCCAGGAACCATGAACGCTGCCTGTGAGCTGC

altered gDNA sequence snippet

CCTCCCATCCCCAGGAACCACGAACGCTGCCTGTGAGCTGC

original cDNA sequence snippet

GCTGGCCACTGGTGGAACCATGAACGCTGCCTGTGAGCTGC

altered cDNA sequence snippet

GCTGGCCACTGGTGGAACCACGAACGCTGCCTGTGAGCTGC

wildtype AA sequence

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGECPVAAS RALPPLRAPR AELEIQKDAL EPGQRVVVVD DLLATGGTMN AACELLGRLQ
AEVLECVSLV ELTSLKGREK LAPVPFFSLL QYE*

mutated AA sequence

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGECPVAAS RALPPLRAPR AELEIQKDAL EPGQRVVVVD DLLATGGTTN AACELLGRLQ
AEVLECVSLV ELTSLKGREK LAPVPFFSLL QYE*

speed

1.37 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

disease causing

Model: simple_aae, prob: 0.999999682191211 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM880009)
known disease mutation: rs18296 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88876242A>GN/A show variant in all transcripts IGV

HGNC symbol

APRT

Ensembl transcript ID

ENST00000378364

Genbank transcript ID

NM_000485

UniProt peptide

P07741

alteration type

single base exchange

alteration region

CDS

DNA changes

c.407T>C
cDNA.452T>C
g.2111T>C

AA changes

M136T Score: 81 explain score(s)

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

136

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.269	1
	4.364	1
(flanking)	2.822	1

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	2105	wt: 0.2583 / mu: 0.3307 (marginal change - not scored)	wt: CCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGTG mu: CCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGTG	cagg\|AACC
Acc marginally increased	2104	wt: 0.8036 / mu: 0.8236 (marginal change - not scored)	wt: ACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGT mu: ACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGT	ccag\|GAAC
Acc marginally increased	2103	wt: 0.9114 / mu: 0.9248 (marginal change - not scored)	wt: GACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTG mu: GACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTG	ccca\|GGAA
Donor increased	2106	wt: 0.47 / mu: 0.70	wt: CCAGGAACCATGAAC mu: CCAGGAACCACGAAC	AGGA\|acca
Donor marginally increased	2103	wt: 0.8481 / mu: 0.8970 (marginal change - not scored)	wt: TCCCCAGGAACCATG mu: TCCCCAGGAACCACG	CCCA\|ggaa
Donor increased	2110	wt: 0.71 / mu: 0.82	wt: GAACCATGAACGCTG mu: GAACCACGAACGCTG	ACCA\|tgaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

136

mutated

not conserved

136

Ptroglodytes

all identical

ENSPTRG00000008466

136

Mmulatta

all identical

ENSMMUG00000013824

136

Fcatus

all identical

ENSFCAG00000018452

109

Mmusculus

all identical

ENSMUSG00000006589

136

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000005211

136

Drerio

all conserved

ENSDARG00000003519

134

Dmelanogaster

all conserved

FBgn0000109

140

Celegans

all conserved

T19B4.3

139

Xtropicalis

all identical

ENSXETG00000027084

136

protein features

start (aa)	end (aa)	feature	details
134	145	HELIX		lost
135	135	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
149	159	STRAND		might get lost (downstream of altered splice site)
160	162	HELIX		might get lost (downstream of altered splice site)
164	168	HELIX		might get lost (downstream of altered splice site)
173	179	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

543 / 543

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

181 / 181

position of stopcodon in wt / mu cDNA

588 / 588

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

46 / 46

chromosome

strand

-1

last intron/exon boundary

446

theoretical NMD boundary in CDS

350

length of CDS

543

coding sequence (CDS) position

407

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

452

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

2111

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

88876242

original gDNA sequence snippet

CCTCCCATCCCCAGGAACCATGAACGCTGCCTGTGAGCTGC

altered gDNA sequence snippet

CCTCCCATCCCCAGGAACCACGAACGCTGCCTGTGAGCTGC

original cDNA sequence snippet

GCTGGCCACTGGTGGAACCATGAACGCTGCCTGTGAGCTGC

altered cDNA sequence snippet

GCTGGCCACTGGTGGAACCACGAACGCTGCCTGTGAGCTGC

wildtype AA sequence

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGGTMNAAC ELLGRLQAEV LECVSLVELT SLKGREKLAP VPFFSLLQYE
*

mutated AA sequence

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGGTTNAAC ELLGRLQAEV LECVSLVELT SLKGREKLAP VPFFSLLQYE
*

speed

1.27 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM880009)
known disease mutation: rs18296 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88876242A>GN/A show variant in all transcripts IGV

HGNC symbol

APRT

Ensembl transcript ID

ENST00000426324

Genbank transcript ID

NM_001030018

UniProt peptide

P07741

alteration type

single base exchange

alteration region

intron

DNA changes

g.2111T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.269	1
	4.364	1
(flanking)	2.822	1

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	2105	wt: 0.2583 / mu: 0.3307 (marginal change - not scored)	wt: CCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGTG mu: CCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGTG	cagg\|AACC
Acc marginally increased	2104	wt: 0.8036 / mu: 0.8236 (marginal change - not scored)	wt: ACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGT mu: ACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGT	ccag\|GAAC
Acc marginally increased	2103	wt: 0.9114 / mu: 0.9248 (marginal change - not scored)	wt: GACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTG mu: GACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTG	ccca\|GGAA
Donor increased	2106	wt: 0.47 / mu: 0.70	wt: CCAGGAACCATGAAC mu: CCAGGAACCACGAAC	AGGA\|acca
Donor marginally increased	2103	wt: 0.8481 / mu: 0.8970 (marginal change - not scored)	wt: TCCCCAGGAACCATG mu: TCCCCAGGAACCACG	CCCA\|ggaa
Donor increased	2110	wt: 0.71 / mu: 0.82	wt: GAACCATGAACGCTG mu: GAACCACGAACGCTG	ACCA\|tgaa

distance from splice site

128

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
134	145	HELIX		might get lost (downstream of altered splice site)
135	135	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
149	159	STRAND		might get lost (downstream of altered splice site)
160	162	HELIX		might get lost (downstream of altered splice site)
164	168	HELIX		might get lost (downstream of altered splice site)
173	179	STRAND		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

27 / 27

chromosome

strand

-1

last intron/exon boundary

427

theoretical NMD boundary in CDS

350

length of CDS

405

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)

2111

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

88876242

original gDNA sequence snippet

CCTCCCATCCCCAGGAACCATGAACGCTGCCTGTGAGCTGC

altered gDNA sequence snippet

CCTCCCATCCCCAGGAACCACGAACGCTGCCTGTGAGCTGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGV*

mutated AA sequence

N/A

speed

1.09 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems