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: ENST00000367922
Querying Taster for transcript #2: ENST00000367921
MT speed 0 s - this script 3.21849 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DDR2	disease_causing_automatic	0.999999999999865	simple_aae		affected	0	R752C	single base exchange	rs121964863		show file
DDR2	disease_causing_automatic	0.999999999999865	simple_aae		affected	0	R752C	single base exchange	rs121964863		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999865 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM090153)
known disease mutation: rs12313 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:162746131C>TN/A show variant in all transcripts IGV

HGNC symbol

DDR2

Ensembl transcript ID

ENST00000367922

Genbank transcript ID

NM_001014796

UniProt peptide

Q16832

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2254C>T
cDNA.2692C>T
g.144969C>T

AA changes

R752C Score: 180 explain score(s)

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

752

frameshift

known variant

Reference ID: rs121964863

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

known disease mutation: rs12313 (pathogenic for Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM090153)

known disease mutation at this position, please check HGMD for details (HGMD ID CM090153)
known disease mutation at this position, please check HGMD for details (HGMD ID CM090153)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.515	1
	5.691	1
(flanking)	5.691	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	144973	wt: 0.8095 / mu: 0.8742 (marginal change - not scored)	wt: GGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGTATCT mu: GGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGTATCT	gctg\|GATG
Acc increased	144974	wt: 0.40 / mu: 0.50	wt: GCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGTATCTT mu: GCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGTATCTT	ctgg\|ATGT
Acc marginally increased	144969	wt: 0.8194 / mu: 0.8198 (marginal change - not scored)	wt: GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT mu: GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT	atcc\|GCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

752

mutated

not conserved

752

Ptroglodytes

all identical

ENSPTRG00000001603

752

Mmulatta

all identical

ENSMMUG00000009330

752

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026674

751

Ggallus

all identical

ENSGALG00000002687

758

Trubripes

all identical

ENSTRUG00000018340

786

Drerio

all identical

ENSDARG00000051913

766

Dmelanogaster

all identical

FBgn0053531

944

GFTGRQ

Celegans

all identical

F11D5.3

687

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
422	855	TOPO_DOM	Cytoplasmic (Potential).	lost
563	849	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2568 / 2568

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

856 / 856

position of stopcodon in wt / mu cDNA

3006 / 3006

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

439 / 439

chromosome

strand

last intron/exon boundary

2872

theoretical NMD boundary in CDS

2383

length of CDS

2568

coding sequence (CDS) position

2254

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

2692

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

144969

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

162746131

original gDNA sequence snippet

GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT

altered gDNA sequence snippet

GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT

original cDNA sequence snippet

GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT

altered cDNA sequence snippet

GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT

wildtype AA sequence

MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LATRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP IRWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*

mutated AA sequence

MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LATRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP ICWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*

speed

0.89 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: 0.999999999999865 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM090153)
known disease mutation: rs12313 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:162746131C>TN/A show variant in all transcripts IGV

HGNC symbol

DDR2

Ensembl transcript ID

ENST00000367921

Genbank transcript ID

NM_006182

UniProt peptide

Q16832

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2254C>T
cDNA.2607C>T
g.144969C>T

AA changes

R752C Score: 180 explain score(s)

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

752

frameshift

known variant

Reference ID: rs121964863

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

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.515	1
	5.691	1
(flanking)	5.691	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	144973	wt: 0.8095 / mu: 0.8742 (marginal change - not scored)	wt: GGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGTATCT mu: GGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGTATCT	gctg\|GATG
Acc increased	144974	wt: 0.40 / mu: 0.50	wt: GCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGTATCTT mu: GCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGTATCTT	ctgg\|ATGT
Acc marginally increased	144969	wt: 0.8194 / mu: 0.8198 (marginal change - not scored)	wt: GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT mu: GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT	atcc\|GCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

752

mutated

not conserved

752

Ptroglodytes

all identical

ENSPTRG00000001603

752

Mmulatta

all identical

ENSMMUG00000009330

752

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026674

751

Ggallus

all identical

ENSGALG00000002687

758

Trubripes

all identical

ENSTRUG00000018340

786

Drerio

all identical

ENSDARG00000051913

766

Dmelanogaster

all identical

FBgn0053531

944

GFTGRQ

Celegans

all identical

F11D5.3

687

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
422	855	TOPO_DOM	Cytoplasmic (Potential).	lost
563	849	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2568 / 2568

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

856 / 856

position of stopcodon in wt / mu cDNA

2921 / 2921

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

354 / 354

chromosome

strand

last intron/exon boundary

2787

theoretical NMD boundary in CDS

2383

length of CDS

2568

coding sequence (CDS) position

2254

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

2607

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

144969

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

162746131

original gDNA sequence snippet

GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT

altered gDNA sequence snippet

GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT

original cDNA sequence snippet

GCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGT

altered cDNA sequence snippet

GCCGGGCAGTGCTCCCTATCTGCTGGATGTCTTGGGAGAGT

wildtype AA sequence

mutated AA sequence

MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LATRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP ICWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*

speed

0.32 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems