MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000442713
Querying Taster for transcript #2: ENST00000269445
MT speed 0 s - this script 3.871444 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DYM	disease_causing_automatic	0.999999999993112	simple_aae		affected	0	C352R	single base exchange	rs120074165		show file
DYM	disease_causing_automatic	0.999999999993112	simple_aae		affected	0	C542R	single base exchange	rs120074165		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999993112 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM093085)
known disease mutation: rs3193 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:46645236A>GN/A show variant in all transcripts IGV

HGNC symbol

DYM

Ensembl transcript ID

ENST00000442713

Genbank transcript ID

N/A

UniProt peptide

Q7RTS9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1054T>C
cDNA.1375T>C
g.342482T>C

AA changes

C352R Score: 180 explain score(s)

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

352

frameshift

known variant

Reference ID: rs120074165
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs3193 (pathogenic for Smith-McCort dysplasia 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.922	1
	4.896	1
(flanking)	1.321	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
Donor increased	342487	wt: 0.66 / mu: 0.82	wt: TGCCTGACAAATTCC mu: CGCCTGACAAATTCC	CCTG\|acaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

352

mutated

not conserved

352

Ptroglodytes

all identical

ENSPTRG00000010011

542

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000012954

542

Mmusculus

all identical

ENSMUSG00000035765

542

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009986

543

Drerio

no homologue

Dmelanogaster

all identical

FBgn0027607

568

Celegans

not conserved

C47D12.2

565

Xtropicalis

all identical

ENSXETG00000020310

543

protein features

start (aa)	end (aa)	feature	details
381	381	CONFLICT	E -> G (in Ref. 3; BAF83992).	might get lost (downstream of altered splice site)
408	408	CONFLICT	D -> Y (in Ref. 4; AAH64394).	might get lost (downstream of altered splice site)
453	453	CONFLICT	R -> K (in Ref. 3; BAF83992).	might get lost (downstream of altered splice site)
458	458	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
537	537	CONFLICT	E -> G (in Ref. 3; BAF83992).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1440 / 1440

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

480 / 480

position of stopcodon in wt / mu cDNA

1761 / 1761

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

322 / 322

chromosome

strand

-1

last intron/exon boundary

1612

theoretical NMD boundary in CDS

1240

length of CDS

1440

coding sequence (CDS) position

1054

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

1375

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

342482

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

46645236

original gDNA sequence snippet

TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC

altered gDNA sequence snippet

TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC

original cDNA sequence snippet

TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC

altered cDNA sequence snippet

TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC

wildtype AA sequence

MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLAGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA PNPYRQAIMS
FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS NIRTYMLART
DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK NITWYSERVL
TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS
LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SCLTNSLHHN
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV ERVLEIIKQG
VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD IQLFTMDSD*

mutated AA sequence

MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLAGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA PNPYRQAIMS
FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS NIRTYMLART
DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK NITWYSERVL
TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS
LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SRLTNSLHHN
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV ERVLEIIKQG
VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD IQLFTMDSD*

speed

1.39 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: 0.999999999993112 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM093085)
known disease mutation: rs3193 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:46645236A>GN/A show variant in all transcripts IGV

HGNC symbol

DYM

Ensembl transcript ID

ENST00000269445

Genbank transcript ID

NM_017653

UniProt peptide

Q7RTS9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1624T>C
cDNA.2082T>C
g.342482T>C

AA changes

C542R Score: 180 explain score(s)

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

542

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.922	1
	4.896	1
(flanking)	1.321	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
Donor increased	342487	wt: 0.66 / mu: 0.82	wt: TGCCTGACAAATTCC mu: CGCCTGACAAATTCC	CCTG\|acaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

542

mutated

not conserved

542

Ptroglodytes

all identical

ENSPTRG00000010011

542

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000012954

542

Mmusculus

all identical

ENSMUSG00000035765

542

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009986

542

Drerio

no homologue

Dmelanogaster

all identical

FBgn0027607

568

Celegans

not conserved

C47D12.2

565

Xtropicalis

all identical

ENSXETG00000020310

543

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2010 / 2010

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

670 / 670

position of stopcodon in wt / mu cDNA

2468 / 2468

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

459 / 459

chromosome

strand

-1

last intron/exon boundary

2319

theoretical NMD boundary in CDS

1810

length of CDS

2010

coding sequence (CDS) position

1624

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

2082

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

342482

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

46645236

original gDNA sequence snippet

TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC

altered gDNA sequence snippet

TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC

original cDNA sequence snippet

TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC

altered cDNA sequence snippet

TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC

wildtype AA sequence

MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS
NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK
NITWYSERVL TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY
AAQRIISLFS LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN
SCLTNSLHHN PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD
IQLFTMDSD*

mutated AA sequence

MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS
NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK
NITWYSERVL TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY
AAQRIISLFS LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN
SRLTNSLHHN PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD
IQLFTMDSD*

speed

0.49 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems