MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
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 3.40198 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL1A1	disease_causing_automatic	0.999999992236817	simple_aae		affected	0	G221C	single base exchange	rs72667037		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999992236817 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM1611482)
known disease mutation at this position (HGMD CM920198)
known disease mutation: rs17320 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:48275128C>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.661G>T
cDNA.780G>T
g.3866G>T

AA changes

G221C Score: 159 explain score(s)

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

221

frameshift

known variant

Reference ID: rs72667037
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17320 (pathogenic for Osteogenesis imperfecta type 1, mild) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1611482)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1611482)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920198)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1611482)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920198)

regulatory features

H3K14ac, Histone, Histone 3 Lysine 14 Acetylation
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
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.13	1
	5.13	1
(flanking)	-0.196	0.992

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	3875	wt: 0.65 / mu: 0.86	wt: TGGGTCCCCGAGGTCCCCCAGGTCCCCCTGGAAAGAATGGA mu: TGGGTCCCCGATGTCCCCCAGGTCCCCCTGGAAAGAATGGA	ccag\|GTCC
Acc marginally increased	3857	wt: 0.9503 / mu: 0.9619 (marginal change - not scored)	wt: ATCTTTTCTAGGGTCCCATGGGTCCCCGAGGTCCCCCAGGT mu: ATCTTTTCTAGGGTCCCATGGGTCCCCGATGTCCCCCAGGT	atgg\|GTCC
Acc increased	3874	wt: 0.21 / mu: 0.63	wt: ATGGGTCCCCGAGGTCCCCCAGGTCCCCCTGGAAAGAATGG mu: ATGGGTCCCCGATGTCCCCCAGGTCCCCCTGGAAAGAATGG	ccca\|GGTC
Donor marginally increased	3870	wt: 0.8143 / mu: 0.8207 (marginal change - not scored)	wt: AGGTCCCCCAGGTCC mu: ATGTCCCCCAGGTCC	GTCC\|ccca
Donor marginally increased	3861	wt: 0.6188 / mu: 0.6650 (marginal change - not scored)	wt: GGGTCCCCGAGGTCC mu: GGGTCCCCGATGTCC	GTCC\|ccga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

221

mutated

not conserved

221

Ptroglodytes

all identical

ENSPTRG00000009393

221

Mmulatta

all identical

ENSMMUG00000001467

221

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000001506

210

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007520

213

Drerio

all identical

ENSDARG00000012405

205

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003374

207

protein features

start (aa)	end (aa)	feature	details
179	1192	REGION	Triple-helical region.	lost
264	266	STRAND		might get lost (downstream of altered splice site)
265	265	MOD_RES	5-hydroxylysine.	might get lost (downstream of altered splice site)
265	265	CARBOHYD	O-linked (Gal...).	might get lost (downstream of altered splice site)
288	288	CONFLICT	E -> P (in Ref. 15; AA sequence).	might get lost (downstream of altered splice site)
370	370	CONFLICT	R -> L (in Ref. 6; AAB59373).	might get lost (downstream of altered splice site)
484	484	CONFLICT	P -> L (in Ref. 19; AAA52289).	might get lost (downstream of altered splice site)
595	595	CONFLICT	A -> R (in Ref. 20; AAA51847).	might get lost (downstream of altered splice site)
721	721	CONFLICT	Q -> E (in Ref. 22; no nucleotide entry).	might get lost (downstream of altered splice site)
738	738	CONFLICT	L -> E (in Ref. 22; no nucleotide entry).	might get lost (downstream of altered splice site)
745	747	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
953	954	SITE	Cleavage; by collagenase (By similarity).	might get lost (downstream of altered splice site)
966	968	STRAND		might get lost (downstream of altered splice site)
975	976	CONFLICT	LP -> PL (in Ref. 19; AAA52291).	might get lost (downstream of altered splice site)
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

661

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

780

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

3866

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

48275128

original gDNA sequence snippet

AGGGTCCCATGGGTCCCCGAGGTCCCCCAGGTCCCCCTGGA

altered gDNA sequence snippet

AGGGTCCCATGGGTCCCCGATGTCCCCCAGGTCCCCCTGGA

original cDNA sequence snippet

CAGGTCCCATGGGTCCCCGAGGTCCCCCAGGTCCCCCTGGA

altered cDNA sequence snippet

CAGGTCCCATGGGTCCCCGATGTCCCCCAGGTCCCCCTGGA

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 CPPGPPGKNG 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*

speed

1.28 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