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: ENST00000225964
MT speed 0 s - this script 3.176491 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL1A1	disease_causing_automatic	0.99999999807443	simple_aae		affected	0	G1082C	single base exchange	rs72656303		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999807443 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM890030)
known disease mutation: rs17299 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:48265474C>AN/A show variant in all transcripts IGV

HGNC symbol

COL1A1

Ensembl transcript ID

ENST00000225964

Genbank transcript ID

NM_000088

UniProt peptide

P02452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3244G>T
cDNA.3363G>T
g.13520G>T

AA changes

G1082C Score: 159 explain score(s)

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

1082

frameshift

known variant

Reference ID: rs72656303
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17299 (pathogenic for Osteogenesis imperfecta, recessive perinatal lethal) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890030)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890030)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890030)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.43	1
	5.43	1
(flanking)	1.415	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	13520	wt: 0.8208 / mu: 0.8641 (marginal change - not scored)	wt: CCGGTCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGTA mu: CCGGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTA	gttg\|GCGC
Acc increased	13526	wt: 0.34 / mu: 0.80	wt: CTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGTAAGTACC mu: CTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTAAGTACC	gccc\|GTGG
Acc increased	13524	wt: 0.21 / mu: 0.82	wt: TCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGTAAGTA mu: TCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTAAGTA	gcgc\|CCGT
Acc increased	13518	wt: 0.22 / mu: 0.41	wt: CACCGGTCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCG mu: CACCGGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCG	ctgt\|TGGC
Acc increased	13528	wt: 0.46 / mu: 0.84	wt: GTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGTAAGTACCCT mu: GTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTAAGTACCCT	ccgt\|GGCC
Acc marginally increased	13516	wt: 0.2662 / mu: 0.3096 (marginal change - not scored)	wt: CCCACCGGTCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGC mu: CCCACCGGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGC	ccct\|GTTG
Acc increased	13530	wt: 0.50 / mu: 0.80	wt: CGGCCCTGTTGGCGCCCGTGGCCCCGCCGTAAGTACCCTGC mu: CGGCCCTGTTTGCGCCCGTGGCCCCGCCGTAAGTACCCTGC	gtgg\|CCCC
Acc gained	13522	0.38	mu: GGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTAAG	ttgc\|GCCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1082

mutated

not conserved

1082

Ptroglodytes

all identical

ENSPTRG00000009393

1082

Mmulatta

all identical

ENSMMUG00000001467

1078

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000001506

1071

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007520

1075

Drerio

all identical

ENSDARG00000012405

1066

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003374

1068

protein features

start (aa)	end (aa)	feature	details
179	1192	REGION	Triple-helical region.	lost
1081	1081	CONFLICT	V -> A (in Ref. 18; AAA51995).	might get lost (downstream of altered splice site)
1093	1095	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
1108	1108	CARBOHYD	O-linked (Gal...) (By similarity).	might get lost (downstream of altered splice site)
1108	1108	MOD_RES	5-hydroxylysine (By similarity).	might get lost (downstream of altered splice site)
1164	1164	MOD_RES	3-hydroxyproline (By similarity).	might get lost (downstream of altered splice site)
1193	1218	REGION	Nonhelical region (C-terminal).	might get lost (downstream of altered splice site)
1208	1208	MOD_RES	Allysine (By similarity).	might get lost (downstream of altered splice site)
1218	1219	SITE	Cleavage; by procollagen C-endopeptidase.	might get lost (downstream of altered splice site)
1219	1464	PROPEP	C-terminal propeptide. /FTId=PRO_0000005721.	might get lost (downstream of altered splice site)
1229	1464	DOMAIN	Fibrillar collagen NC1.	might get lost (downstream of altered splice site)
1259	1259	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1259	1259	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1265	1265	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1265	1265	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1282	1282	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1282	1282	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1291	1291	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1291	1291	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1299	1299	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1329	1329	CONFLICT	S -> T (in Ref. 25; AAB27856).	might get lost (downstream of altered splice site)
1365	1365	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1370	1370	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1415	1415	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1462	1462	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4395 / 4395

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

1465 / 1465

position of stopcodon in wt / mu cDNA

4514 / 4514

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

120 / 120

chromosome

strand

-1

last intron/exon boundary

4368

theoretical NMD boundary in CDS

4198

length of CDS

4395

coding sequence (CDS) position

3244

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

3363

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

13520

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

48265474

original gDNA sequence snippet

CCGGTCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGTA

altered gDNA sequence snippet

CCGGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGTA

original cDNA sequence snippet

CCGGTCCTGTCGGCCCTGTTGGCGCCCGTGGCCCCGCCGGA

altered cDNA sequence snippet

CCGGTCCTGTCGGCCCTGTTTGCGCCCGTGGCCCCGCCGGA

wildtype AA sequence

MFSFVDLRLL LLLAATALLT HGQEEGQVEG QDEDIPPITC VQNGLRYHDR DVWKPEPCRI
CVCDNGKVLC DDVICDETKN CPGAEVPEGE CCPVCPDGSE SPTDQETTGV EGPKGDTGPR
GPRGPAGPPG RDGIPGQPGL PGPPGPPGPP GPPGLGGNFA PQLSYGYDEK STGGISVPGP
MGPSGPRGLP GPPGAPGPQG FQGPPGEPGE PGASGPMGPR GPPGPPGKNG DDGEAGKPGR
PGERGPPGPQ GARGLPGTAG LPGMKGHRGF SGLDGAKGDA GPAGPKGEPG SPGENGAPGQ
MGPRGLPGER GRPGAPGPAG ARGNDGATGA AGPPGPTGPA GPPGFPGAVG AKGEAGPQGP
RGSEGPQGVR GEPGPPGPAG AAGPAGNPGA DGQPGAKGAN GAPGIAGAPG FPGARGPSGP
QGPGGPPGPK GNSGEPGAPG SKGDTGAKGE PGPVGVQGPP GPAGEEGKRG ARGEPGPTGL
PGPPGERGGP GSRGFPGADG VAGPKGPAGE RGSPGPAGPK GSPGEAGRPG EAGLPGAKGL
TGSPGSPGPD GKTGPPGPAG QDGRPGPPGP PGARGQAGVM GFPGPKGAAG EPGKAGERGV
PGPPGAVGPA GKDGEAGAQG PPGPAGPAGE RGEQGPAGSP GFQGLPGPAG PPGEAGKPGE
QGVPGDLGAP GPSGARGERG FPGERGVQGP PGPAGPRGAN GAPGNDGAKG DAGAPGAPGS
QGAPGLQGMP GERGAAGLPG PKGDRGDAGP KGADGSPGKD GVRGLTGPIG PPGPAGAPGD
KGESGPSGPA GPTGARGAPG DRGEPGPPGP AGFAGPPGAD GQPGAKGEPG DAGAKGDAGP
PGPAGPAGPP GPIGNVGAPG AKGARGSAGP PGATGFPGAA GRVGPPGPSG NAGPPGPPGP
AGKEGGKGPR GETGPAGRPG EVGPPGPPGP AGEKGSPGAD GPAGAPGTPG PQGIAGQRGV
VGLPGQRGER GFPGLPGPSG EPGKQGPSGA SGERGPPGPM GPPGLAGPPG ESGREGAPGA
EGSPGRDGSP GAKGDRGETG PAGPPGAPGA PGAPGPVGPA GKSGDRGETG PAGPTGPVGP
VGARGPAGPQ GPRGDKGETG EQGDRGIKGH RGFSGLQGPP GPPGSPGEQG PSGASGPAGP
RGPPGSAGAP GKDGLNGLPG PIGPPGPRGR TGDAGPVGPP GPPGPPGPPG PPSAGFDFSF
LPQPPQEKAH DGGRYYRADD ANVVRDRDLE VDTTLKSLSQ QIENIRSPEG SRKNPARTCR
DLKMCHSDWK SGEYWIDPNQ GCNLDAIKVF CNMETGETCV YPTQPSVAQK NWYISKNPKD
KRHVWFGESM TDGFQFEYGG QGSDPADVAI QLTFLRLMST EASQNITYHC KNSVAYMDQQ
TGNLKKALLL QGSNEIEIRA EGNSRFTYSV TVDGCTSHTG AWGKTVIEYK TTKTSRLPII
DVAPLDVGAP DQEFGFDVGP VCFL*

mutated AA sequence

MFSFVDLRLL LLLAATALLT HGQEEGQVEG QDEDIPPITC VQNGLRYHDR DVWKPEPCRI
CVCDNGKVLC DDVICDETKN CPGAEVPEGE CCPVCPDGSE SPTDQETTGV EGPKGDTGPR
GPRGPAGPPG RDGIPGQPGL PGPPGPPGPP GPPGLGGNFA PQLSYGYDEK STGGISVPGP
MGPSGPRGLP GPPGAPGPQG FQGPPGEPGE PGASGPMGPR GPPGPPGKNG DDGEAGKPGR
PGERGPPGPQ GARGLPGTAG LPGMKGHRGF SGLDGAKGDA GPAGPKGEPG SPGENGAPGQ
MGPRGLPGER GRPGAPGPAG ARGNDGATGA AGPPGPTGPA GPPGFPGAVG AKGEAGPQGP
RGSEGPQGVR GEPGPPGPAG AAGPAGNPGA DGQPGAKGAN GAPGIAGAPG FPGARGPSGP
QGPGGPPGPK GNSGEPGAPG SKGDTGAKGE PGPVGVQGPP GPAGEEGKRG ARGEPGPTGL
PGPPGERGGP GSRGFPGADG VAGPKGPAGE RGSPGPAGPK GSPGEAGRPG EAGLPGAKGL
TGSPGSPGPD GKTGPPGPAG QDGRPGPPGP PGARGQAGVM GFPGPKGAAG EPGKAGERGV
PGPPGAVGPA GKDGEAGAQG PPGPAGPAGE RGEQGPAGSP GFQGLPGPAG PPGEAGKPGE
QGVPGDLGAP GPSGARGERG FPGERGVQGP PGPAGPRGAN GAPGNDGAKG DAGAPGAPGS
QGAPGLQGMP GERGAAGLPG PKGDRGDAGP KGADGSPGKD GVRGLTGPIG PPGPAGAPGD
KGESGPSGPA GPTGARGAPG DRGEPGPPGP AGFAGPPGAD GQPGAKGEPG DAGAKGDAGP
PGPAGPAGPP GPIGNVGAPG AKGARGSAGP PGATGFPGAA GRVGPPGPSG NAGPPGPPGP
AGKEGGKGPR GETGPAGRPG EVGPPGPPGP AGEKGSPGAD GPAGAPGTPG PQGIAGQRGV
VGLPGQRGER GFPGLPGPSG EPGKQGPSGA SGERGPPGPM GPPGLAGPPG ESGREGAPGA
EGSPGRDGSP GAKGDRGETG PAGPPGAPGA PGAPGPVGPA GKSGDRGETG PAGPTGPVGP
VCARGPAGPQ GPRGDKGETG EQGDRGIKGH RGFSGLQGPP GPPGSPGEQG PSGASGPAGP
RGPPGSAGAP GKDGLNGLPG PIGPPGPRGR TGDAGPVGPP GPPGPPGPPG PPSAGFDFSF
LPQPPQEKAH DGGRYYRADD ANVVRDRDLE VDTTLKSLSQ QIENIRSPEG SRKNPARTCR
DLKMCHSDWK SGEYWIDPNQ GCNLDAIKVF CNMETGETCV YPTQPSVAQK NWYISKNPKD
KRHVWFGESM TDGFQFEYGG QGSDPADVAI QLTFLRLMST EASQNITYHC KNSVAYMDQQ
TGNLKKALLL QGSNEIEIRA EGNSRFTYSV TVDGCTSHTG AWGKTVIEYK TTKTSRLPII
DVAPLDVGAP DQEFGFDVGP VCFL*

speed

1.06 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