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: ENST00000432161
Querying Taster for transcript #2: ENST00000411726
Querying Taster for transcript #3: ENST00000242375
MT speed 0 s - this script 3.49904 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AKR1D1	disease_causing	0.999999999712693	simple_aae		affected		P198L	single base exchange	rs121918342		show file
AKR1D1	disease_causing	0.999999999712693	simple_aae		affected		P198L	single base exchange	rs121918342		show file
AKR1D1	disease_causing	0.999999999952858	simple_aae		affected		P157L	single base exchange	rs121918342		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999712693 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5374 (probable pathogenic)
known disease mutation at this position (HGMD CM032543)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:137791367C>TN/A show variant in all transcripts IGV

HGNC symbol

AKR1D1

Ensembl transcript ID

ENST00000432161

Genbank transcript ID

NM_001190907

UniProt peptide

P51857

alteration type

single base exchange

alteration region

CDS

DNA changes

c.593C>T
cDNA.680C>T
g.104298C>T

AA changes

P198L Score: 98 explain score(s)

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

198

frameshift

known variant

Reference ID: rs121918342

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

known as potential disease variant: rs5374 (probable pathogenic for Congenital bile acid synthesis defect 2|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032543)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032543)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032543)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.964	1
	4.964	1
(flanking)	-0.801	0.882

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 increased	104309	wt: 0.61 / mu: 0.74	wt: AGTGCCATCCGTATTTCACCCAGCCAAAACTCTTGAAATTT mu: AGTGCCATCTGTATTTCACCCAGCCAAAACTCTTGAAATTT	accc\|AGCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

198

mutated

not conserved

198

Ptroglodytes

all identical

ENSPTRG00000019740

198

Mmulatta

all identical

ENSMMUG00000005422

198

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038641

197

Ggallus

all identical

ENSGALG00000012834

198

Trubripes

all identical

ENSTRUG00000016401

198

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026269

199

protein features

start (aa)	end (aa)	feature	details
203	211	HELIX		might get lost (downstream of altered splice site)
215	220	STRAND		might get lost (downstream of altered splice site)
220	224	NP_BIND	NADP.	might get lost (downstream of altered splice site)
228	230	TURN		might get lost (downstream of altered splice site)
230	230	BINDING	Substrate.	might get lost (downstream of altered splice site)
238	240	HELIX		might get lost (downstream of altered splice site)
242	250	HELIX		might get lost (downstream of altered splice site)
255	265	HELIX		might get lost (downstream of altered splice site)
273	283	NP_BIND	NADP.	might get lost (downstream of altered splice site)
277	284	HELIX		might get lost (downstream of altered splice site)
293	300	HELIX		might get lost (downstream of altered splice site)
312	314	HELIX		might get lost (downstream of altered splice site)
321	324	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

873 / 873

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

291 / 291

position of stopcodon in wt / mu cDNA

960 / 960

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

88 / 88

chromosome

strand

last intron/exon boundary

943

theoretical NMD boundary in CDS

805

length of CDS

873

coding sequence (CDS) position

593

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

680

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

104298

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

137791367

original gDNA sequence snippet

CACATAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered gDNA sequence snippet

CACATAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

original cDNA sequence snippet

CAACCAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered cDNA sequence snippet

CAACCAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

wildtype AA sequence

MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHPYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQVARSS *

mutated AA sequence

MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHLYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQVARSS *

speed

0.15 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: 0.999999999712693 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5374 (probable pathogenic)
known disease mutation at this position (HGMD CM032543)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:137791367C>TN/A show variant in all transcripts IGV

HGNC symbol

AKR1D1

Ensembl transcript ID

ENST00000242375

Genbank transcript ID

NM_005989

UniProt peptide

P51857

alteration type

single base exchange

alteration region

CDS

DNA changes

c.593C>T
cDNA.635C>T
g.104298C>T

AA changes

P198L Score: 98 explain score(s)

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

198

frameshift

known variant

Reference ID: rs121918342

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.964	1
	4.964	1
(flanking)	-0.801	0.882

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 increased	104309	wt: 0.61 / mu: 0.74	wt: AGTGCCATCCGTATTTCACCCAGCCAAAACTCTTGAAATTT mu: AGTGCCATCTGTATTTCACCCAGCCAAAACTCTTGAAATTT	accc\|AGCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

198

mutated

not conserved

198

Ptroglodytes

all identical

ENSPTRG00000019740

198

Mmulatta

all identical

ENSMMUG00000005422

198

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038641

197

Ggallus

all identical

ENSGALG00000012834

198

Trubripes

all identical

ENSTRUG00000016401

198

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026269

199

protein features

start (aa)	end (aa)	feature	details
203	211	HELIX		might get lost (downstream of altered splice site)
215	220	STRAND		might get lost (downstream of altered splice site)
220	224	NP_BIND	NADP.	might get lost (downstream of altered splice site)
228	230	TURN		might get lost (downstream of altered splice site)
230	230	BINDING	Substrate.	might get lost (downstream of altered splice site)
238	240	HELIX		might get lost (downstream of altered splice site)
242	250	HELIX		might get lost (downstream of altered splice site)
255	265	HELIX		might get lost (downstream of altered splice site)
273	283	NP_BIND	NADP.	might get lost (downstream of altered splice site)
277	284	HELIX		might get lost (downstream of altered splice site)
293	300	HELIX		might get lost (downstream of altered splice site)
312	314	HELIX		might get lost (downstream of altered splice site)
321	324	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

981 / 981

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

327 / 327

position of stopcodon in wt / mu cDNA

1023 / 1023

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

43 / 43

chromosome

strand

last intron/exon boundary

981

theoretical NMD boundary in CDS

888

length of CDS

981

coding sequence (CDS) position

593

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

635

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

104298

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

137791367

original gDNA sequence snippet

CACATAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered gDNA sequence snippet

CACATAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

original cDNA sequence snippet

CAACCAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered cDNA sequence snippet

CAACCAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

wildtype AA sequence

mutated AA sequence

MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHLYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQIFDFS LTEEEMKDIE
ALNKNVRFVE LLMWRDHPEY PFHDEY*

speed

1.29 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999952858 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5374 (probable pathogenic)
known disease mutation at this position (HGMD CM032543)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:137791367C>TN/A show variant in all transcripts IGV

HGNC symbol

AKR1D1

Ensembl transcript ID

ENST00000411726

Genbank transcript ID

NM_001190906

UniProt peptide

P51857

alteration type

single base exchange

alteration region

CDS

DNA changes

c.470C>T
cDNA.522C>T
g.104298C>T

AA changes

P157L Score: 98 explain score(s)

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

157

frameshift

known variant

Reference ID: rs121918342

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.964	1
	4.964	1
(flanking)	-0.801	0.882

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 increased	104309	wt: 0.61 / mu: 0.74	wt: AGTGCCATCCGTATTTCACCCAGCCAAAACTCTTGAAATTT mu: AGTGCCATCTGTATTTCACCCAGCCAAAACTCTTGAAATTT	accc\|AGCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

157

mutated

not conserved

157

Ptroglodytes

all identical

ENSPTRG00000019740

185

NKPGLKHKPVSNQ

Mmulatta

all identical

ENSMMUG00000005422

185

NKPGLKYKPVSNQ

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038641

184

NKPGLKYKPVTNQ

Ggallus

all identical

ENSGALG00000012834

185

NKPGLKHKPVSNQ

Trubripes

all identical

ENSTRUG00000016401

185

NKPGLKYKPVSNQ

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026269

185

LNKPGLKYKPATNQ

protein features

start (aa)	end (aa)	feature	details
147	159	HELIX		lost
162	170	STRAND		might get lost (downstream of altered splice site)
169	170	NP_BIND	NADP.	might get lost (downstream of altered splice site)
173	180	HELIX		might get lost (downstream of altered splice site)
191	195	STRAND		might get lost (downstream of altered splice site)
193	193	BINDING	NADP.	might get lost (downstream of altered splice site)
203	211	HELIX		might get lost (downstream of altered splice site)
215	220	STRAND		might get lost (downstream of altered splice site)
220	224	NP_BIND	NADP.	might get lost (downstream of altered splice site)
228	230	TURN		might get lost (downstream of altered splice site)
230	230	BINDING	Substrate.	might get lost (downstream of altered splice site)
238	240	HELIX		might get lost (downstream of altered splice site)
242	250	HELIX		might get lost (downstream of altered splice site)
255	265	HELIX		might get lost (downstream of altered splice site)
273	283	NP_BIND	NADP.	might get lost (downstream of altered splice site)
277	284	HELIX		might get lost (downstream of altered splice site)
293	300	HELIX		might get lost (downstream of altered splice site)
312	314	HELIX		might get lost (downstream of altered splice site)
321	324	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

858 / 858

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

286 / 286

position of stopcodon in wt / mu cDNA

910 / 910

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

53 / 53

chromosome

strand

last intron/exon boundary

868

theoretical NMD boundary in CDS

765

length of CDS

858

coding sequence (CDS) position

470

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

522

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

104298

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

137791367

original gDNA sequence snippet

CACATAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered gDNA sequence snippet

CACATAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

original cDNA sequence snippet

TTGGGAGGTTGAGTGCCATCCGTATTTCACCCAGCCAAAAC

altered cDNA sequence snippet

TTGGGAGGTTGAGTGCCATCTGTATTTCACCCAGCCAAAAC

wildtype AA sequence

MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEVECHPYFT QPKLLKFCQQ HDIVITAYSP
LGTSRNPIWV NVSSPPLLKD ALLNSLGKRY NKTAAQIVLR FNIQRGVVVI PKSFNLERIK
ENFQIFDFSL TEEEMKDIEA LNKNVRFVEL LMWRDHPEYP FHDEY*

mutated AA sequence

MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEVECHLYFT QPKLLKFCQQ HDIVITAYSP
LGTSRNPIWV NVSSPPLLKD ALLNSLGKRY NKTAAQIVLR FNIQRGVVVI PKSFNLERIK
ENFQIFDFSL TEEEMKDIEA LNKNVRFVEL LMWRDHPEYP FHDEY*

speed

0.17 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