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 2.822188 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL1A1	disease_causing_automatic	0.999999996944483	simple_aae		affected	0	L1464P	single base exchange	rs72656353		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999996944483 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960324)
known disease mutation: rs17332 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:48262867A>GN/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.4391T>C
cDNA.4510T>C
g.16127T>C

AA changes

L1464P Score: 98 explain score(s)

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

1464

frameshift

known variant

Reference ID: rs72656353
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17332 (pathogenic for Osteogenesis imperfecta type III) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960324)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960324)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960324)

regulatory features

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)	5.337	1
	4.22	1
(flanking)	0.64	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	16128	wt: 0.7673 / mu: 0.7966 (marginal change - not scored)	wt: GTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCATCCCAAC mu: GTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCATCCCAAC	cctg\|TAAA
Acc increased	16124	wt: 0.60 / mu: 0.71	wt: CGACGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCATCC mu: CGACGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCATCC	gctt\|CCTG
Acc increased	16121	wt: 0.29 / mu: 0.39	wt: CTTCGACGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCA mu: CTTCGACGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCA	tctg\|CTTC
Acc marginally increased	16120	wt: 0.4938 / mu: 0.5332 (marginal change - not scored)	wt: GCTTCGACGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCC mu: GCTTCGACGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCC	gtct\|GCTT
Acc marginally increased	16127	wt: 0.9260 / mu: 0.9290 (marginal change - not scored)	wt: CGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCATCCCAA mu: CGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCATCCCAA	tcct\|GTAA
Donor marginally increased	16127	wt: 0.9732 / mu: 0.9916 (marginal change - not scored)	wt: CTTCCTGTAAACTCC mu: CTTCCCGTAAACTCC	TCCT\|gtaa

distance from splice site

143

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1464

mutated

no alignment

n/a

Ptroglodytes

all identical

ENSPTRG00000009393

1464

Mmulatta

all identical

ENSMMUG00000001467

1460

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000001506

1453

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007520

1457

Drerio

all identical

ENSDARG00000012405

1447

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000003374

1449

protein features

start (aa)	end (aa)	feature	details
1219	1464	PROPEP	C-terminal propeptide. /FTId=PRO_0000005721.	lost
1229	1464	DOMAIN	Fibrillar collagen NC1.	lost
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

4391

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

4510

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

16127

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

48262867

original gDNA sequence snippet

CGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCATCCCAA

altered gDNA sequence snippet

CGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCATCCCAA

original cDNA sequence snippet

CGTTGGCCCTGTCTGCTTCCTGTAAACTCCCTCCATCCCAA

altered cDNA sequence snippet

CGTTGGCCCTGTCTGCTTCCCGTAAACTCCCTCCATCCCAA

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

speed

0.72 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