MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000377270
Querying Taster for transcript #2: ENST00000396366
Querying Taster for transcript #3: ENST00000498653
Querying Taster for transcript #4: ENST00000396364
MT speed 0 s - this script 4.091545 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FXN	disease_causing	0.999999999960955	simple_aae				R90C	single base exchange	rs138034837		show file
FXN	disease_causing	0.999999999991379	simple_aae				R165C	single base exchange	rs138034837		show file
FXN	disease_causing	1	without_aae					single base exchange	rs138034837		show file
FXN	disease_causing	1	without_aae					single base exchange	rs138034837		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999960955 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002020)
known disease mutation at this position (HGMD CX163073)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:71687538C>TN/A show variant in all transcripts IGV

HGNC symbol

FXN

Ensembl transcript ID

ENST00000498653

Genbank transcript ID

N/A

UniProt peptide

Q16595

alteration type

single base exchange

alteration region

CDS

DNA changes

c.268C>T
cDNA.373C>T
g.37364C>T

AA changes

R90C Score: 180 explain score(s)

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

frameshift

known variant

Reference ID: rs138034837
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)

known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)

known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.293	1
	5.515	1
(flanking)	5.515	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	37354	wt: 0.7657 / mu: 0.7916 (marginal change - not scored)	wt: GCATTTGTTTTGTCTTCCAGTGGACCTAAGCGTTATGACTG mu: GCATTTGTTTTGTCTTCCAGTGGACCTAAGTGTTATGACTG	cagt\|GGAC
Donor marginally increased	37357	wt: 0.9864 / mu: 0.9958 (marginal change - not scored)	wt: AGTGGACCTAAGCGT mu: AGTGGACCTAAGTGT	TGGA\|ccta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000000357

165

Fcatus

all identical

ENSFCAG00000008813

163

Mmusculus

all identical

ENSMUSG00000059363

162

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074356

159

Dmelanogaster

all identical

FBgn0030092

143

TVAAG

Celegans

all identical

F59G1.7

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

408 / 408

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

136 / 136

position of stopcodon in wt / mu cDNA

513 / 513

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

106 / 106

chromosome

strand

last intron/exon boundary

363

theoretical NMD boundary in CDS

207

length of CDS

408

coding sequence (CDS) position

268

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

373

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

37364

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

71687538

original gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

original cDNA sequence snippet

CTCCATCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered cDNA sequence snippet

CTCCATCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

wildtype AA sequence

MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA*

mutated AA sequence

MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKC YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA*

speed

0.44 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: 0.999999999991379 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002020)
known disease mutation at this position (HGMD CX163073)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:71687538C>TN/A show variant in all transcripts IGV

HGNC symbol

FXN

Ensembl transcript ID

ENST00000377270

Genbank transcript ID

NM_000144

UniProt peptide

Q16595

alteration type

single base exchange

alteration region

CDS

DNA changes

c.493C>T
cDNA.1017C>T
g.37364C>T

AA changes

R165C Score: 180 explain score(s)

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

165

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.293	1
	5.515	1
(flanking)	5.515	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	37354	wt: 0.7657 / mu: 0.7916 (marginal change - not scored)	wt: GCATTTGTTTTGTCTTCCAGTGGACCTAAGCGTTATGACTG mu: GCATTTGTTTTGTCTTCCAGTGGACCTAAGTGTTATGACTG	cagt\|GGAC
Donor marginally increased	37357	wt: 0.9864 / mu: 0.9958 (marginal change - not scored)	wt: AGTGGACCTAAGCGT mu: AGTGGACCTAAGTGT	TGGA\|ccta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

165

mutated

not conserved

165

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000000357

165

Fcatus

all identical

ENSFCAG00000008813

163

Mmusculus

all identical

ENSMUSG00000059363

162

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074356

159

Dmelanogaster

all identical

FBgn0030092

143

TVAAG

Celegans

all identical

F59G1.7

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
164	168	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

633 / 633

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

211 / 211

position of stopcodon in wt / mu cDNA

1157 / 1157

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

525 / 525

chromosome

strand

last intron/exon boundary

1007

theoretical NMD boundary in CDS

432

length of CDS

633

coding sequence (CDS) position

493

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

1017

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

37364

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

71687538

original gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

original cDNA sequence snippet

CTCCATCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered cDNA sequence snippet

CTCCATCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

wildtype AA sequence

MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS SGPKRYDWTG KNWVYSHDGV
SLHELLAAEL TKALKTKLDL SSLAYSGKDA *

mutated AA sequence

MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS SGPKCYDWTG KNWVYSHDGV
SLHELLAAEL TKALKTKLDL SSLAYSGKDA *

speed

1.37 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known disease mutation at this position (HGMD CM002020)
known disease mutation at this position (HGMD CX163073)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:71687538C>TN/A show variant in all transcripts IGV

HGNC symbol

FXN

Ensembl transcript ID

ENST00000396366

Genbank transcript ID

NM_181425

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.501C>T
cDNA.522C>T
g.37364C>T

AA changes

no AA changes

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

N/A

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.293	1
	5.515	1
(flanking)	5.515	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	37354	wt: 0.7657 / mu: 0.7916 (marginal change - not scored)	wt: GCATTTGTTTTGTCTTCCAGTGGACCTAAGCGTTATGACTG mu: GCATTTGTTTTGTCTTCCAGTGGACCTAAGTGTTATGACTG	cagt\|GGAC
Donor marginally increased	37357	wt: 0.9864 / mu: 0.9958 (marginal change - not scored)	wt: AGTGGACCTAAGCGT mu: AGTGGACCTAAGTGT	TGGA\|ccta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

591 / 591

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

197 / 197

position of stopcodon in wt / mu cDNA

612 / 612

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

last intron/exon boundary

512

theoretical NMD boundary in CDS

440

length of CDS

591

coding sequence (CDS) position

501

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

522

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

37364

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

71687538

original gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

original cDNA sequence snippet

AGGTATGTAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered cDNA sequence snippet

AGGTATGTAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

wildtype AA sequence

mutated AA sequence

speed

0.76 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known disease mutation at this position (HGMD CM002020)
known disease mutation at this position (HGMD CX163073)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:71687538C>TN/A show variant in all transcripts IGV

HGNC symbol

FXN

Ensembl transcript ID

ENST00000396364

Genbank transcript ID

NM_001161706

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.37364C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.293	1
	5.515	1
(flanking)	5.515	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	37354	wt: 0.7657 / mu: 0.7916 (marginal change - not scored)	wt: GCATTTGTTTTGTCTTCCAGTGGACCTAAGCGTTATGACTG mu: GCATTTGTTTTGTCTTCCAGTGGACCTAAGTGTTATGACTG	cagt\|GGAC
Donor marginally increased	37357	wt: 0.9864 / mu: 0.9958 (marginal change - not scored)	wt: AGTGGACCTAAGCGT mu: AGTGGACCTAAGTGT	TGGA\|ccta

distance from splice site

7587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

221 / 221

chromosome

strand

last intron/exon boundary

703

theoretical NMD boundary in CDS

432

length of CDS

516

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)

37364

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

71687538

original gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RLTWLLWLFH P*

mutated AA sequence

N/A

speed

0.35 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

Problems