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: ENST00000251081
Querying Taster for transcript #2: ENST00000280904
MT speed 0 s - this script 3.678228 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DSC2	polymorphism_automatic	8.30446822419617e-14	simple_aae		affected		I776V	single base exchange	rs1893963		show file
DSC2	polymorphism_automatic	1.36002320516582e-13	simple_aae		affected		I776V	single base exchange	rs1893963		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999917 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:28649042T>CN/A show variant in all transcripts IGV

HGNC symbol

DSC2

Ensembl transcript ID

ENST00000251081

Genbank transcript ID

NM_004949

UniProt peptide

Q02487

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2326A>G
cDNA.2359A>G
g.33337A>G

AA changes

I776V Score: 29 explain score(s)

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

776

frameshift

known variant

Reference ID: rs1893963

database	homozygous (C/C)	heterozygous	allele carriers
1000G	165	654	819
ExAC	1499	11439	12938

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.328	0.047
	0.472	0.113
(flanking)	0.402	0.239

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	33328	wt: 0.22 / mu: 0.31	wt: AGGGAGTTTGTGGCACCGTGGGATCAGGAATCAAAAACGGA mu: AGGGAGTTTGTGGCACCGTGGGATCAGGAGTCAAAAACGGA	gtgg\|GATC
Donor gained	33336	0.99	mu: TCAGGAGTCAAAAAC	AGGA\|gtca
Donor gained	33331	0.92	mu: TGGGATCAGGAGTCA	GGAT\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

776

mutated

all conserved

776

Ptroglodytes

all conserved

ENSPTRG00000009941

789

Mmulatta

all conserved

ENSMMUG00000011687

776

Fcatus

all conserved

ENSFCAG00000000644

754

Mmusculus

all conserved

ENSMUSG00000024331

776

Ggallus

all identical

ENSGALG00000015140

745

Trubripes

not conserved

ENSTRUG00000007388

772

AGAKGTL

Drerio

no alignment

ENSDARG00000039677

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000004721

776

protein features

start (aa)	end (aa)	feature	details
716	901	TOPO_DOM	Cytoplasmic (Potential).	lost
864	864	MOD_RES	Phosphoserine (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2544 / 2544

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

848 / 848

position of stopcodon in wt / mu cDNA

2577 / 2577

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

34 / 34

chromosome

strand

-1

last intron/exon boundary

2588

theoretical NMD boundary in CDS

2504

length of CDS

2544

coding sequence (CDS) position

2326

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

2359

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

33337

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

28649042

original gDNA sequence snippet

GTGGCACCGTGGGATCAGGAATCAAAAACGGAGGTCAGGAG

altered gDNA sequence snippet

GTGGCACCGTGGGATCAGGAGTCAAAAACGGAGGTCAGGAG

original cDNA sequence snippet

GTGGCACCGTGGGATCAGGAATCAAAAACGGAGGTCAGGAG

altered cDNA sequence snippet

GTGGCACCGTGGGATCAGGAGTCAAAAACGGAGGTCAGGAG

wildtype AA sequence

MEAARPSGSW NGALCRLLLL TLAILIFASD ACKNVTLHVP SKLDAEKLVG RVNLKECFTA
ANLIHSSDPD FQILEDGSVY TTNTILLSSE KRSFTILLSN TENQEKKKIF VFLEHQTKVL
KKRHTKEKVL RRAKRRWAPI PCSMLENSLG PFPLFLQQVQ SDTAQNYTIY YSIRGPGVDQ
EPRNLFYVER DTGNLYCTRP VDREQYESFE IIAFATTPDG YTPELPLPLI IKIEDENDNY
PIFTEETYTF TIFENCRVGT TVGQVCATDK DEPDTMHTRL KYSIIGQVPP SPTLFSMHPT
TGVITTTSSQ LDRELIDKYQ LKIKVQDMDG QYFGLQTTST CIINIDDVND HLPTFTRTSY
VTSVEENTVD VEILRVTVED KDLVNTANWR ANYTILKGNE NGNFKIVTDA KTNEGVLCVV
KPLNYEEKQQ MILQIGVVNE APFSREASPR SAMSTATVTV NVEDQDEGPE CNPPIQTVRM
KENAEVGTTS NGYKAYDPET RSSSGIRYKK LTDPTGWVTI DENTGSIKVF RSLDREAETI
KNGIYNITVL ASDQGGRTCT GTLGIILQDV NDNSPFIPKK TVIICKPTMS SAEIVAVDPD
EPIHGPPFDF SLESSTSEVQ RMWRLKAIND TAARLSYQND PPFGSYVVPI TVRDRLGMSS
VTSLDVTLCD CITENDCTHR VDPRIGGGGV QLGKWAILAI LLGIALLFCI LFTLVCGASG
TSKQPKVIPD DLAQQNLIVS NTEAPGDDKV YSANGFTTQT VGASAQGVCG TVGSGIKNGG
QETIEMVKGG HQTSESCRGA GHHHTLDSCR GGHTEVDNCR YTYSEWHSFT QPRLGEESIR
GHTLIKN*

mutated AA sequence

MEAARPSGSW NGALCRLLLL TLAILIFASD ACKNVTLHVP SKLDAEKLVG RVNLKECFTA
ANLIHSSDPD FQILEDGSVY TTNTILLSSE KRSFTILLSN TENQEKKKIF VFLEHQTKVL
KKRHTKEKVL RRAKRRWAPI PCSMLENSLG PFPLFLQQVQ SDTAQNYTIY YSIRGPGVDQ
EPRNLFYVER DTGNLYCTRP VDREQYESFE IIAFATTPDG YTPELPLPLI IKIEDENDNY
PIFTEETYTF TIFENCRVGT TVGQVCATDK DEPDTMHTRL KYSIIGQVPP SPTLFSMHPT
TGVITTTSSQ LDRELIDKYQ LKIKVQDMDG QYFGLQTTST CIINIDDVND HLPTFTRTSY
VTSVEENTVD VEILRVTVED KDLVNTANWR ANYTILKGNE NGNFKIVTDA KTNEGVLCVV
KPLNYEEKQQ MILQIGVVNE APFSREASPR SAMSTATVTV NVEDQDEGPE CNPPIQTVRM
KENAEVGTTS NGYKAYDPET RSSSGIRYKK LTDPTGWVTI DENTGSIKVF RSLDREAETI
KNGIYNITVL ASDQGGRTCT GTLGIILQDV NDNSPFIPKK TVIICKPTMS SAEIVAVDPD
EPIHGPPFDF SLESSTSEVQ RMWRLKAIND TAARLSYQND PPFGSYVVPI TVRDRLGMSS
VTSLDVTLCD CITENDCTHR VDPRIGGGGV QLGKWAILAI LLGIALLFCI LFTLVCGASG
TSKQPKVIPD DLAQQNLIVS NTEAPGDDKV YSANGFTTQT VGASAQGVCG TVGSGVKNGG
QETIEMVKGG HQTSESCRGA GHHHTLDSCR GGHTEVDNCR YTYSEWHSFT QPRLGEESIR
GHTLIKN*

speed

0.66 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

polymorphism

Model: simple_aae, prob: 0.999999999999864 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:28649042T>CN/A show variant in all transcripts IGV

HGNC symbol

DSC2

Ensembl transcript ID

ENST00000280904

Genbank transcript ID

NM_024422

UniProt peptide

Q02487

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2326A>G
cDNA.2770A>G
g.33337A>G

AA changes

I776V Score: 29 explain score(s)

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

776

frameshift

known variant

Reference ID: rs1893963

database	homozygous (C/C)	heterozygous	allele carriers
1000G	165	654	819
ExAC	1499	11439	12938

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.328	0.047
	0.472	0.113
(flanking)	0.402	0.239

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	33328	wt: 0.22 / mu: 0.31	wt: AGGGAGTTTGTGGCACCGTGGGATCAGGAATCAAAAACGGA mu: AGGGAGTTTGTGGCACCGTGGGATCAGGAGTCAAAAACGGA	gtgg\|GATC
Donor gained	33336	0.99	mu: TCAGGAGTCAAAAAC	AGGA\|gtca
Donor gained	33331	0.92	mu: TGGGATCAGGAGTCA	GGAT\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

776

mutated

all conserved

776

Ptroglodytes

all conserved

ENSPTRG00000009941

789

Mmulatta

all conserved

ENSMMUG00000011687

776

Fcatus

all conserved

ENSFCAG00000000644

754

Mmusculus

all conserved

ENSMUSG00000024331

776

Ggallus

all identical

ENSGALG00000015140

745

Trubripes

not conserved

ENSTRUG00000007388

772

AGAKGTL

Drerio

all conserved

ENSDARG00000039677

795

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000004721

776

protein features

start (aa)	end (aa)	feature	details
716	901	TOPO_DOM	Cytoplasmic (Potential).	lost
864	864	MOD_RES	Phosphoserine (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2706 / 2706

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

902 / 902

position of stopcodon in wt / mu cDNA

3150 / 3150

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

445 / 445

chromosome

strand

-1

last intron/exon boundary

2953

theoretical NMD boundary in CDS

2458

length of CDS

2706

coding sequence (CDS) position

2326

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

2770

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

33337

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

28649042

original gDNA sequence snippet

GTGGCACCGTGGGATCAGGAATCAAAAACGGAGGTCAGGAG

altered gDNA sequence snippet

GTGGCACCGTGGGATCAGGAGTCAAAAACGGAGGTCAGGAG

original cDNA sequence snippet

GTGGCACCGTGGGATCAGGAATCAAAAACGGAGGTCAGGAG

altered cDNA sequence snippet

GTGGCACCGTGGGATCAGGAGTCAAAAACGGAGGTCAGGAG

wildtype AA sequence

mutated AA sequence

MEAARPSGSW NGALCRLLLL TLAILIFASD ACKNVTLHVP SKLDAEKLVG RVNLKECFTA
ANLIHSSDPD FQILEDGSVY TTNTILLSSE KRSFTILLSN TENQEKKKIF VFLEHQTKVL
KKRHTKEKVL RRAKRRWAPI PCSMLENSLG PFPLFLQQVQ SDTAQNYTIY YSIRGPGVDQ
EPRNLFYVER DTGNLYCTRP VDREQYESFE IIAFATTPDG YTPELPLPLI IKIEDENDNY
PIFTEETYTF TIFENCRVGT TVGQVCATDK DEPDTMHTRL KYSIIGQVPP SPTLFSMHPT
TGVITTTSSQ LDRELIDKYQ LKIKVQDMDG QYFGLQTTST CIINIDDVND HLPTFTRTSY
VTSVEENTVD VEILRVTVED KDLVNTANWR ANYTILKGNE NGNFKIVTDA KTNEGVLCVV
KPLNYEEKQQ MILQIGVVNE APFSREASPR SAMSTATVTV NVEDQDEGPE CNPPIQTVRM
KENAEVGTTS NGYKAYDPET RSSSGIRYKK LTDPTGWVTI DENTGSIKVF RSLDREAETI
KNGIYNITVL ASDQGGRTCT GTLGIILQDV NDNSPFIPKK TVIICKPTMS SAEIVAVDPD
EPIHGPPFDF SLESSTSEVQ RMWRLKAIND TAARLSYQND PPFGSYVVPI TVRDRLGMSS
VTSLDVTLCD CITENDCTHR VDPRIGGGGV QLGKWAILAI LLGIALLFCI LFTLVCGASG
TSKQPKVIPD DLAQQNLIVS NTEAPGDDKV YSANGFTTQT VGASAQGVCG TVGSGVKNGG
QETIEMVKGG HQTSESCRGA GHHHTLDSCR GGHTEVDNCR YTYSEWHSFT QPRLGEKVYL
CNQDENHKHA QDYVLTYNYE GRGSVAGSVG CCSERQEEDG LEFLDNLEPK FRTLAEACMK
R*

speed

1.02 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems