MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000297268
MT speed 0 s - this script 3.161672 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL1A2	disease_causing_automatic	0.999999998527948	simple_aae		affected	0	G661S	single base exchange	rs72658152		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998527948 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM070864)
known disease mutation at this position (HGMD CM123312)
known disease mutation: rs17258 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:94047820G>AN/A show variant in all transcripts IGV

HGNC symbol

COL1A2

Ensembl transcript ID

ENST00000297268

Genbank transcript ID

NM_000089

UniProt peptide

P08123

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1981G>A
cDNA.2452G>A
g.23948G>A

AA changes

G661S Score: 56 explain score(s)

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

661

frameshift

known variant

Reference ID: rs72658152
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17258 (pathogenic for Postmenopausal osteoporosis) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070864)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070864)
known disease mutation at this position, please check HGMD for details (HGMD ID CM123312)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070864)
known disease mutation at this position, please check HGMD for details (HGMD ID CM123312)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070864)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.845	1
	6.35	1
(flanking)	4.648	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 decreased	23938	wt: 0.9465 / mu: 0.9244 (marginal change - not scored)	wt: GCTCTTGCTTTATACTTTCAGGGTGAACCTGGTCTCAGAGG mu: GCTCTTGCTTTATACTTTCAGGGTGAACCTAGTCTCAGAGG	tcag\|GGTG
Donor increased	23939	wt: 0.55 / mu: 0.68	wt: TTCAGGGTGAACCTG mu: TTCAGGGTGAACCTA	CAGG\|gtga
Donor gained	23943	0.79	mu: GGGTGAACCTAGTCT	GTGA\|acct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

661

mutated

not conserved

661

Ptroglodytes

all identical

ENSPTRG00000019409

661

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029661

667

Ggallus

all identical

ENSGALG00000009641

660

Trubripes

all identical

ENSTRUG00000015407

726

Drerio

all identical

ENSDARG00000020007

651

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020318

658

protein features

start (aa)	end (aa)	feature	details
828	828	CONFLICT	V -> A (in Ref. 17; CAA23761).	might get lost (downstream of altered splice site)
831	831	CONFLICT	T -> P (in Ref. 17; CAA23761).	might get lost (downstream of altered splice site)
837	837	CONFLICT	V -> P (in Ref. 17; CAA23761).	might get lost (downstream of altered splice site)
980	980	CONFLICT	E -> V (in Ref. 21; AAA51996).	might get lost (downstream of altered splice site)
1098	1098	CONFLICT	P -> L (in Ref. 17; CAA23761).	might get lost (downstream of altered splice site)
1103	1366	PROPEP	C-terminal propeptide. /FTId=PRO_0000005806.	might get lost (downstream of altered splice site)
1122	1125	CONFLICT	Missing (in Ref. 17; CAA23761).	might get lost (downstream of altered splice site)
1133	1366	DOMAIN	Fibrillar collagen NC1.	might get lost (downstream of altered splice site)
1267	1267	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1338	1338	CONFLICT	R -> A (in Ref. 23; AAA51887).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4101 / 4101

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

1367 / 1367

position of stopcodon in wt / mu cDNA

4572 / 4572

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

472 / 472

chromosome

strand

last intron/exon boundary

4426

theoretical NMD boundary in CDS

3904

length of CDS

4101

coding sequence (CDS) position

1981

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

2452

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

23948

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

94047820

original gDNA sequence snippet

TATACTTTCAGGGTGAACCTGGTCTCAGAGGTGAAATTGGT

altered gDNA sequence snippet

TATACTTTCAGGGTGAACCTAGTCTCAGAGGTGAAATTGGT

original cDNA sequence snippet

AGGGAGAAAAGGGTGAACCTGGTCTCAGAGGTGAAATTGGT

altered cDNA sequence snippet

AGGGAGAAAAGGGTGAACCTAGTCTCAGAGGTGAAATTGGT

wildtype AA sequence

MLSFVDTRTL LLLAVTLCLA TCQSLQEETV RKGPAGDRGP RGERGPPGPP GRDGEDGPTG
PPGPPGPPGP PGLGGNFAAQ YDGKGVGLGP GPMGLMGPRG PPGAAGAPGP QGFQGPAGEP
GEPGQTGPAG ARGPAGPPGK AGEDGHPGKP GRPGERGVVG PQGARGFPGT PGLPGFKGIR
GHNGLDGLKG QPGAPGVKGE PGAPGENGTP GQTGARGLPG ERGRVGAPGP AGARGSDGSV
GPVGPAGPIG SAGPPGFPGA PGPKGEIGAV GNAGPAGPAG PRGEVGLPGL SGPVGPPGNP
GANGLTGAKG AAGLPGVAGA PGLPGPRGIP GPVGAAGATG ARGLVGEPGP AGSKGESGNK
GEPGSAGPQG PPGPSGEEGK RGPNGEAGSA GPPGPPGLRG SPGSRGLPGA DGRAGVMGPP
GSRGASGPAG VRGPNGDAGR PGEPGLMGPR GLPGSPGNIG PAGKEGPVGL PGIDGRPGPI
GPAGARGEPG NIGFPGPKGP TGDPGKNGDK GHAGLAGARG APGPDGNNGA QGPPGPQGVQ
GGKGEQGPPG PPGFQGLPGP SGPAGEVGKP GERGLHGEFG LPGPAGPRGE RGPPGESGAA
GPTGPIGSRG PSGPPGPDGN KGEPGVVGAV GTAGPSGPSG LPGERGAAGI PGGKGEKGEP
GLRGEIGNPG RDGARGAPGA VGAPGPAGAT GDRGEAGAAG PAGPAGPRGS PGERGEVGPA
GPNGFAGPAG AAGQPGAKGE RGAKGPKGEN GVVGPTGPVG AAGPAGPNGP PGPAGSRGDG
GPPGMTGFPG AAGRTGPPGP SGISGPPGPP GPAGKEGLRG PRGDQGPVGR TGEVGAVGPP
GFAGEKGPSG EAGTAGPPGT PGPQGLLGAP GILGLPGSRG ERGLPGVAGA VGEPGPLGIA
GPPGARGPPG AVGSPGVNGA PGEAGRDGNP GNDGPPGRDG QPGHKGERGY PGNIGPVGAA
GAPGPHGPVG PAGKHGNRGE TGPSGPVGPA GAVGPRGPSG PQGIRGDKGE PGEKGPRGLP
GLKGHNGLQG LPGIAGHHGD QGAPGSVGPA GPRGPAGPSG PAGKDGRTGH PGTVGPAGIR
GPQGHQGPAG PPGPPGPPGP PGVSGGGYDF GYDGDFYRAD QPRSAPSLRP KDYEVDATLK
SLNNQIETLL TPEGSRKNPA RTCRDLRLSH PEWSSGYYWI DPNQGCTMDA IKVYCDFSTG
ETCIRAQPEN IPAKNWYRSS KDKKHVWLGE TINAGSQFEY NVEGVTSKEM ATQLAFMRLL
ANYASQNITY HCKNSIAYMD EETGNLKKAV ILQGSNDVEL VAEGNSRFTY TVLVDGCSKK
TNEWGKTIIE YKTNKPSRLP FLDIAPLDIG GADQEFFVDI GPVCFK*

mutated AA sequence

MLSFVDTRTL LLLAVTLCLA TCQSLQEETV RKGPAGDRGP RGERGPPGPP GRDGEDGPTG
PPGPPGPPGP PGLGGNFAAQ YDGKGVGLGP GPMGLMGPRG PPGAAGAPGP QGFQGPAGEP
GEPGQTGPAG ARGPAGPPGK AGEDGHPGKP GRPGERGVVG PQGARGFPGT PGLPGFKGIR
GHNGLDGLKG QPGAPGVKGE PGAPGENGTP GQTGARGLPG ERGRVGAPGP AGARGSDGSV
GPVGPAGPIG SAGPPGFPGA PGPKGEIGAV GNAGPAGPAG PRGEVGLPGL SGPVGPPGNP
GANGLTGAKG AAGLPGVAGA PGLPGPRGIP GPVGAAGATG ARGLVGEPGP AGSKGESGNK
GEPGSAGPQG PPGPSGEEGK RGPNGEAGSA GPPGPPGLRG SPGSRGLPGA DGRAGVMGPP
GSRGASGPAG VRGPNGDAGR PGEPGLMGPR GLPGSPGNIG PAGKEGPVGL PGIDGRPGPI
GPAGARGEPG NIGFPGPKGP TGDPGKNGDK GHAGLAGARG APGPDGNNGA QGPPGPQGVQ
GGKGEQGPPG PPGFQGLPGP SGPAGEVGKP GERGLHGEFG LPGPAGPRGE RGPPGESGAA
GPTGPIGSRG PSGPPGPDGN KGEPGVVGAV GTAGPSGPSG LPGERGAAGI PGGKGEKGEP
SLRGEIGNPG RDGARGAPGA VGAPGPAGAT GDRGEAGAAG PAGPAGPRGS PGERGEVGPA
GPNGFAGPAG AAGQPGAKGE RGAKGPKGEN GVVGPTGPVG AAGPAGPNGP PGPAGSRGDG
GPPGMTGFPG AAGRTGPPGP SGISGPPGPP GPAGKEGLRG PRGDQGPVGR TGEVGAVGPP
GFAGEKGPSG EAGTAGPPGT PGPQGLLGAP GILGLPGSRG ERGLPGVAGA VGEPGPLGIA
GPPGARGPPG AVGSPGVNGA PGEAGRDGNP GNDGPPGRDG QPGHKGERGY PGNIGPVGAA
GAPGPHGPVG PAGKHGNRGE TGPSGPVGPA GAVGPRGPSG PQGIRGDKGE PGEKGPRGLP
GLKGHNGLQG LPGIAGHHGD QGAPGSVGPA GPRGPAGPSG PAGKDGRTGH PGTVGPAGIR
GPQGHQGPAG PPGPPGPPGP PGVSGGGYDF GYDGDFYRAD QPRSAPSLRP KDYEVDATLK
SLNNQIETLL TPEGSRKNPA RTCRDLRLSH PEWSSGYYWI DPNQGCTMDA IKVYCDFSTG
ETCIRAQPEN IPAKNWYRSS KDKKHVWLGE TINAGSQFEY NVEGVTSKEM ATQLAFMRLL
ANYASQNITY HCKNSIAYMD EETGNLKKAV ILQGSNDVEL VAEGNSRFTY TVLVDGCSKK
TNEWGKTIIE YKTNKPSRLP FLDIAPLDIG GADQEFFVDI GPVCFK*

speed

1.05 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems