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 3.110477 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL1A1	disease_causing	0.999998784860263	simple_aae		affected		G1195C	single base exchange	rs72656334		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998784860263 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM880016)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:48264232C>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.3583G>T
cDNA.3702G>T
g.14762G>T

AA changes

G1195C Score: 159 explain score(s)

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

1195

frameshift

known variant

Reference ID: rs72656334
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM880016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880016)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.459	1
	3.483	1
(flanking)	-0.126	0.985

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	14762	wt: 0.5449 / mu: 0.5874 (marginal change - not scored)	wt: CCCCTGGTCCTCCCAGCGCTGGTTTCGACTTCAGCTTCCTG mu: CCCCTGGTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTG	gctg\|GTTT
Acc marginally increased	14758	wt: 0.4751 / mu: 0.4886 (marginal change - not scored)	wt: GGTCCCCCTGGTCCTCCCAGCGCTGGTTTCGACTTCAGCTT mu: GGTCCCCCTGGTCCTCCCAGCGCTTGTTTCGACTTCAGCTT	cagc\|GCTG
Acc gained	14764	0.55	mu: CCTGGTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTGCC	ttgt\|TTCG
Acc gained	14768	0.42	mu: GTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTGCCCCAG	ttcg\|ACTT
Acc gained	14767	0.69	mu: GGTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTGCCCCA	tttc\|GACT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1195

mutated

not conserved

1195

Ptroglodytes

all identical

ENSPTRG00000009393

1195

Mmulatta

all identical

ENSMMUG00000001467

1191

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000001506

1184

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007520

1188

Drerio

all identical

ENSDARG00000012405

1179

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003374

1181

protein features

start (aa)	end (aa)	feature	details
1193	1218	REGION	Nonhelical region (C-terminal).	lost
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

3583

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

3702

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

14762

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

48264232

original gDNA sequence snippet

CCCCTGGTCCTCCCAGCGCTGGTTTCGACTTCAGCTTCCTG

altered gDNA sequence snippet

CCCCTGGTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTG

original cDNA sequence snippet

CCCCTGGTCCTCCCAGCGCTGGTTTCGACTTCAGCTTCCTG

altered cDNA sequence snippet

CCCCTGGTCCTCCCAGCGCTTGTTTCGACTTCAGCTTCCTG

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
VGARGPAGPQ GPRGDKGETG EQGDRGIKGH RGFSGLQGPP GPPGSPGEQG PSGASGPAGP
RGPPGSAGAP GKDGLNGLPG PIGPPGPRGR TGDAGPVGPP GPPGPPGPPG PPSACFDFSF
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

1.05 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