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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000335606
Querying Taster for transcript #2: ENST00000382072
Querying Taster for transcript #3: ENST00000382085
Querying Taster for transcript #4: ENST00000502637
Querying Taster for transcript #5: ENST00000441713
MT speed 0 s - this script 4.328259 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AMACR	disease_causing_automatic	0.999999999980732	simple_aae		affected	0	L107P	single base exchange	rs121917816		show file
AMACR	disease_causing_automatic	0.999999999980732	simple_aae		affected	0	L107P	single base exchange	rs121917816		show file
AMACR	disease_causing_automatic	0.999999999980732	simple_aae		affected	0	L107P	single base exchange	rs121917816		show file
AMACR	disease_causing_automatic	0.999999999980732	simple_aae		affected	0	L107P	single base exchange	rs121917816		show file
AMACR	disease_causing_automatic	0.999999999980732	simple_aae		affected	0	L107P	single base exchange	rs121917816		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000501)
known disease mutation: rs5524 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:34005932A>GN/A show variant in all transcripts IGV

HGNC symbol

AMACR

Ensembl transcript ID

ENST00000335606

Genbank transcript ID

NM_014324

UniProt peptide

Q9UHK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.320T>C
cDNA.409T>C
g.2289T>C

AA changes

L107P Score: 98 explain score(s)

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

107

frameshift

known variant

Reference ID: rs121917816

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs5524 (pathogenic for Congenital bile acid synthesis defect 4) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.286	0.98
	3.474	0.978
(flanking)	0.1	0.364

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	2286	wt: 0.23 / mu: 0.29	wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT	ccag\|GCTG
Donor marginally increased	2286	wt: 0.9779 / mu: 0.9794 (marginal change - not scored)	wt: TGCCAGGCTGAGTGG mu: TGCCAGGCCGAGTGG	CCAG\|gctg
Donor marginally increased	2291	wt: 0.6556 / mu: 0.7170 (marginal change - not scored)	wt: GGCTGAGTGGATTTG mu: GGCCGAGTGGATTTG	CTGA\|gtgg
Donor increased	2281	wt: 0.88 / mu: 0.97	wt: ATTTATGCCAGGCTG mu: ATTTATGCCAGGCCG	TTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000013467

107

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022244

106

Ggallus

all identical

ENSGALG00000003326

108

Trubripes

all identical

ENSTRUG00000014396

107

Drerio

all identical

ENSDARG00000057435

107

Dmelanogaster

all identical

FBgn0032881

106

Celegans

all conserved

C24A3.4

108

Xtropicalis

all identical

ENSXETG00000002559

107

protein features

start (aa)	end (aa)	feature	details
128	128	CONFLICT	A -> T (in Ref. 6; ABQ59031).	might get lost (downstream of altered splice site)
150	150	CONFLICT	L -> V (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
152	152	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
183	183	CONFLICT	N -> D (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
257	257	CONFLICT	N -> S (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
327	327	CONFLICT	P -> L (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
340	342	CONFLICT	FKR -> SKG (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
380	382	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1149 / 1149

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

383 / 383

position of stopcodon in wt / mu cDNA

1238 / 1238

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

829

theoretical NMD boundary in CDS

689

length of CDS

1149

coding sequence (CDS) position

320

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

409

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

2289

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

34005932

original gDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered gDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

original cDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered cDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

wildtype AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARLSGF GQSGSFCRLA
GHDINYLALS GVLSKIGRSG ENPYAPLNLL ADFAGGGLMC ALGIIMALFD RTRTGKGQVI
DANMVEGTAY LSSFLWKTQK LSLWEAPRGQ NMLDGGAPFY TTYRTADGEF MAVGAIEPQF
YELLIKGLGL KSDELPNQMS MDDWPEMKKK FADVFAEKTK AEWCQIFDGT DACVTPVLTF
EEVVHHDHNK ERGSFITSEE QDVSPRPAPL LLNTPAIPSF KRDPFIGEHT EEILEEFGFS
REEIYQLNSD KIIESNKVKA SL*

mutated AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARPSGF GQSGSFCRLA
GHDINYLALS GVLSKIGRSG ENPYAPLNLL ADFAGGGLMC ALGIIMALFD RTRTGKGQVI
DANMVEGTAY LSSFLWKTQK LSLWEAPRGQ NMLDGGAPFY TTYRTADGEF MAVGAIEPQF
YELLIKGLGL KSDELPNQMS MDDWPEMKKK FADVFAEKTK AEWCQIFDGT DACVTPVLTF
EEVVHHDHNK ERGSFITSEE QDVSPRPAPL LLNTPAIPSF KRDPFIGEHT EEILEEFGFS
REEIYQLNSD KIIESNKVKA SL*

speed

0.50 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: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000501)
known disease mutation: rs5524 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:34005932A>GN/A show variant in all transcripts IGV

HGNC symbol

AMACR

Ensembl transcript ID

ENST00000382072

Genbank transcript ID

NM_203382

UniProt peptide

Q9UHK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.320T>C
cDNA.332T>C
g.2289T>C

AA changes

L107P Score: 98 explain score(s)

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

107

frameshift

known variant

Reference ID: rs121917816

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.286	0.98
	3.474	0.978
(flanking)	0.1	0.364

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	2286	wt: 0.23 / mu: 0.29	wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT	ccag\|GCTG
Donor marginally increased	2286	wt: 0.9779 / mu: 0.9794 (marginal change - not scored)	wt: TGCCAGGCTGAGTGG mu: TGCCAGGCCGAGTGG	CCAG\|gctg
Donor marginally increased	2291	wt: 0.6556 / mu: 0.7170 (marginal change - not scored)	wt: GGCTGAGTGGATTTG mu: GGCCGAGTGGATTTG	CTGA\|gtgg
Donor increased	2281	wt: 0.88 / mu: 0.97	wt: ATTTATGCCAGGCTG mu: ATTTATGCCAGGCCG	TTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000013467

107

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022244

106

Ggallus

all identical

ENSGALG00000003326

108

Trubripes

all identical

ENSTRUG00000014396

107

Drerio

all identical

ENSDARG00000057435

107

Dmelanogaster

all identical

FBgn0032881

106

Celegans

all conserved

C24A3.4

108

Xtropicalis

all identical

ENSXETG00000002559

107

protein features

start (aa)	end (aa)	feature	details
128	128	CONFLICT	A -> T (in Ref. 6; ABQ59031).	might get lost (downstream of altered splice site)
150	150	CONFLICT	L -> V (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
152	152	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
183	183	CONFLICT	N -> D (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
257	257	CONFLICT	N -> S (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
327	327	CONFLICT	P -> L (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
340	342	CONFLICT	FKR -> SKG (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
380	382	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

597 / 597

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

199 / 199

position of stopcodon in wt / mu cDNA

609 / 609

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

13 / 13

chromosome

strand

-1

last intron/exon boundary

591

theoretical NMD boundary in CDS

528

length of CDS

597

coding sequence (CDS) position

320

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

332

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

2289

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

34005932

original gDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered gDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

original cDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered cDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

wildtype AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARLSGF GQSGSFCRLA
GHDINYLALS GGRNSIFKFF SVENSEIESV GSTSRTEHVG WWSTFLYDLQ DSRWGIHGCW
SNRTPVLRAA DQRTWTKV*

mutated AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARPSGF GQSGSFCRLA
GHDINYLALS GGRNSIFKFF SVENSEIESV GSTSRTEHVG WWSTFLYDLQ DSRWGIHGCW
SNRTPVLRAA DQRTWTKV*

speed

1.15 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000501)
known disease mutation: rs5524 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:34005932A>GN/A show variant in all transcripts IGV

HGNC symbol

AMACR

Ensembl transcript ID

ENST00000382085

Genbank transcript ID

NM_001167595

UniProt peptide

Q9UHK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.320T>C
cDNA.329T>C
g.2289T>C

AA changes

L107P Score: 98 explain score(s)

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

107

frameshift

known variant

Reference ID: rs121917816

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.286	0.98
	3.474	0.978
(flanking)	0.1	0.364

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	2286	wt: 0.23 / mu: 0.29	wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT	ccag\|GCTG
Donor marginally increased	2286	wt: 0.9779 / mu: 0.9794 (marginal change - not scored)	wt: TGCCAGGCTGAGTGG mu: TGCCAGGCCGAGTGG	CCAG\|gctg
Donor marginally increased	2291	wt: 0.6556 / mu: 0.7170 (marginal change - not scored)	wt: GGCTGAGTGGATTTG mu: GGCCGAGTGGATTTG	CTGA\|gtgg
Donor increased	2281	wt: 0.88 / mu: 0.97	wt: ATTTATGCCAGGCTG mu: ATTTATGCCAGGCCG	TTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000013467

107

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022244

106

Ggallus

all identical

ENSGALG00000003326

108

Trubripes

all identical

ENSTRUG00000014396

107

Drerio

all identical

ENSDARG00000057435

107

Dmelanogaster

all identical

FBgn0032881

106

Celegans

all conserved

C24A3.4

108

Xtropicalis

all identical

ENSXETG00000002559

107

protein features

start (aa)	end (aa)	feature	details
128	128	CONFLICT	A -> T (in Ref. 6; ABQ59031).	might get lost (downstream of altered splice site)
150	150	CONFLICT	L -> V (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
152	152	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
183	183	CONFLICT	N -> D (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
257	257	CONFLICT	N -> S (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
327	327	CONFLICT	P -> L (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
340	342	CONFLICT	FKR -> SKG (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
380	382	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1185 / 1185

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

395 / 395

position of stopcodon in wt / mu cDNA

1194 / 1194

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

10 / 10

chromosome

strand

-1

last intron/exon boundary

1141

theoretical NMD boundary in CDS

1081

length of CDS

1185

coding sequence (CDS) position

320

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

329

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

2289

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

34005932

original gDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered gDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

original cDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered cDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

wildtype AA sequence

mutated AA sequence

speed

0.48 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000501)
known disease mutation: rs5524 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:34005932A>GN/A show variant in all transcripts IGV

HGNC symbol

AMACR

Ensembl transcript ID

ENST00000502637

Genbank transcript ID

N/A

UniProt peptide

Q9UHK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.320T>C
cDNA.405T>C
g.2289T>C

AA changes

L107P Score: 98 explain score(s)

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

107

frameshift

known variant

Reference ID: rs121917816

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.286	0.98
	3.474	0.978
(flanking)	0.1	0.364

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	2286	wt: 0.23 / mu: 0.29	wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT	ccag\|GCTG
Donor marginally increased	2286	wt: 0.9779 / mu: 0.9794 (marginal change - not scored)	wt: TGCCAGGCTGAGTGG mu: TGCCAGGCCGAGTGG	CCAG\|gctg
Donor marginally increased	2291	wt: 0.6556 / mu: 0.7170 (marginal change - not scored)	wt: GGCTGAGTGGATTTG mu: GGCCGAGTGGATTTG	CTGA\|gtgg
Donor increased	2281	wt: 0.88 / mu: 0.97	wt: ATTTATGCCAGGCTG mu: ATTTATGCCAGGCCG	TTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000013467

107

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022244

106

Ggallus

all identical

ENSGALG00000003326

108

Trubripes

all identical

ENSTRUG00000014396

107

Drerio

all identical

ENSDARG00000057435

107

Dmelanogaster

all identical

FBgn0032881

106

Celegans

all conserved

C24A3.4

108

Xtropicalis

all identical

ENSXETG00000002559

107

protein features

start (aa)	end (aa)	feature	details
128	128	CONFLICT	A -> T (in Ref. 6; ABQ59031).	might get lost (downstream of altered splice site)
150	150	CONFLICT	L -> V (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
152	152	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
183	183	CONFLICT	N -> D (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
257	257	CONFLICT	N -> S (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
327	327	CONFLICT	P -> L (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
340	342	CONFLICT	FKR -> SKG (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
380	382	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

position of stopcodon in wt / mu cDNA

1189 / 1189

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

86 / 86

chromosome

strand

-1

last intron/exon boundary

780

theoretical NMD boundary in CDS

644

length of CDS

1104

coding sequence (CDS) position

320

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

405

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

2289

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

34005932

original gDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered gDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

original cDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered cDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

wildtype AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARLSGF GQSGSFCRLA
GHDINYLALS GVLSKIGRSG ENPYAPLNLL ADFAGGGLMC ALGIIMALFD RTRTGKGQVI
DANMKLSLWE APRGQNMLDG GAPFYTTYRT ADGEFMAVGA IEPQFYELLI KGLGLKSDEL
PNQMSMDDWP EMKKKFADVF AEKTKAEWCQ IFDGTDACVT PVLTFEEVVH HDHNKERGSF
ITSEEQDVSP RPAPLLLNTP AIPSFKRDPF IGEHTEEILE EFGFSREEIY QLNSDKIIES
NKVKASL*

mutated AA sequence

MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARPSGF GQSGSFCRLA
GHDINYLALS GVLSKIGRSG ENPYAPLNLL ADFAGGGLMC ALGIIMALFD RTRTGKGQVI
DANMKLSLWE APRGQNMLDG GAPFYTTYRT ADGEFMAVGA IEPQFYELLI KGLGLKSDEL
PNQMSMDDWP EMKKKFADVF AEKTKAEWCQ IFDGTDACVT PVLTFEEVVH HDHNKERGSF
ITSEEQDVSP RPAPLLLNTP AIPSFKRDPF IGEHTEEILE EFGFSREEIY QLNSDKIIES
NKVKASL*

speed

1.14 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000501)
known disease mutation: rs5524 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:34005932A>GN/A show variant in all transcripts IGV

HGNC symbol

AMACR

Ensembl transcript ID

ENST00000441713

Genbank transcript ID

N/A

UniProt peptide

Q9UHK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.320T>C
cDNA.416T>C
g.2289T>C

AA changes

L107P Score: 98 explain score(s)

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

107

frameshift

known variant

Reference ID: rs121917816

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.286	0.98
	3.474	0.978
(flanking)	0.1	0.364

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	2286	wt: 0.23 / mu: 0.29	wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT	ccag\|GCTG
Donor marginally increased	2286	wt: 0.9779 / mu: 0.9794 (marginal change - not scored)	wt: TGCCAGGCTGAGTGG mu: TGCCAGGCCGAGTGG	CCAG\|gctg
Donor marginally increased	2291	wt: 0.6556 / mu: 0.7170 (marginal change - not scored)	wt: GGCTGAGTGGATTTG mu: GGCCGAGTGGATTTG	CTGA\|gtgg
Donor increased	2281	wt: 0.88 / mu: 0.97	wt: ATTTATGCCAGGCTG mu: ATTTATGCCAGGCCG	TTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000013467

107

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022244

106

Ggallus

all identical

ENSGALG00000003326

108

Trubripes

all identical

ENSTRUG00000014396

107

Drerio

all identical

ENSDARG00000057435

107

Dmelanogaster

all identical

FBgn0032881

106

Celegans

all conserved

C24A3.4

108

Xtropicalis

all identical

ENSXETG00000002559

107

protein features

start (aa)	end (aa)	feature	details
128	128	CONFLICT	A -> T (in Ref. 6; ABQ59031).	might get lost (downstream of altered splice site)
150	150	CONFLICT	L -> V (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
152	152	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
183	183	CONFLICT	N -> D (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
257	257	CONFLICT	N -> S (in Ref. 3; AAD10205).	might get lost (downstream of altered splice site)
327	327	CONFLICT	P -> L (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
340	342	CONFLICT	FKR -> SKG (in Ref. 1; CAB44062).	might get lost (downstream of altered splice site)
380	382	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

690 / 690

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

230 / 230

position of stopcodon in wt / mu cDNA

786 / 786

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

97 / 97

chromosome

strand

-1

last intron/exon boundary

675

theoretical NMD boundary in CDS

528

length of CDS

690

coding sequence (CDS) position

320

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

416

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

2289

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

34005932

original gDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered gDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

original cDNA sequence snippet

AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG

altered cDNA sequence snippet

AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG

wildtype AA sequence

mutated AA sequence

speed

0.48 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

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems