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: ENST00000372330
MT speed 0 s - this script 2.797291 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MMP9	polymorphism_automatic	0.012061539377082	simple_aae		affected		Q279R	single base exchange	rs17576		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.987938460622918 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM062877)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:44640225A>GN/A show variant in all transcripts IGV

HGNC symbol

MMP9

Ensembl transcript ID

ENST00000372330

Genbank transcript ID

NM_004994

UniProt peptide

P14780

alteration type

single base exchange

alteration region

CDS

DNA changes

c.836A>G
cDNA.855A>G
g.2679A>G

AA changes

Q279R Score: 43 explain score(s)

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

279

frameshift

known variant

Reference ID: rs17576

database	homozygous (G/G)	heterozygous	allele carriers
1000G	590	1101	1691
ExAC	10209	12349	22558

known disease mutation at this position, please check HGMD for details (HGMD ID CM062877)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.453	0.999
	1.452	1
(flanking)	0.932	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	2674	wt: 0.3165 / mu: 0.3440 (marginal change - not scored)	wt: CTCCTCGCCCCAGGACTCTACACCCAGGACGGCAATGCTGA mu: CTCCTCGCCCCAGGACTCTACACCCGGGACGGCAATGCTGA	ctac\|ACCC
Donor increased	2678	wt: 0.26 / mu: 0.98	wt: ACACCCAGGACGGCA mu: ACACCCGGGACGGCA	ACCC\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

279

mutated

all conserved

279

Ptroglodytes

all identical

ENSPTRG00000013577

279

Mmulatta

all identical

ENSMMUG00000016549

279

Fcatus

all identical

ENSFCAG00000014014

105

Mmusculus

all conserved

ENSMUSG00000017737

279

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000000827

281

Drerio

not conserved

ENSDARG00000042816

280

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000033145

276

protein features

start (aa)	end (aa)	feature	details
279	283	STRAND		lost
283	331	DOMAIN	Fibronectin type-II 2.	might get lost (downstream of altered splice site)
288	288	DISULFID	By similarity.	might get lost (downstream of altered splice site)
290	294	STRAND		might get lost (downstream of altered splice site)
297	301	STRAND		might get lost (downstream of altered splice site)
302	302	DISULFID	By similarity.	might get lost (downstream of altered splice site)
313	319	STRAND		might get lost (downstream of altered splice site)
314	314	DISULFID	By similarity.	might get lost (downstream of altered splice site)
320	323	HELIX		might get lost (downstream of altered splice site)
326	328	STRAND		might get lost (downstream of altered splice site)
329	329	DISULFID	By similarity.	might get lost (downstream of altered splice site)
333	335	HELIX		might get lost (downstream of altered splice site)
340	344	TURN		might get lost (downstream of altered splice site)
342	390	DOMAIN	Fibronectin type-II 3.	might get lost (downstream of altered splice site)
347	347	DISULFID	By similarity.	might get lost (downstream of altered splice site)
349	353	STRAND		might get lost (downstream of altered splice site)
356	358	STRAND		might get lost (downstream of altered splice site)
361	361	DISULFID	By similarity.	might get lost (downstream of altered splice site)
372	378	STRAND		might get lost (downstream of altered splice site)
373	373	DISULFID	By similarity.	might get lost (downstream of altered splice site)
379	382	HELIX		might get lost (downstream of altered splice site)
385	387	STRAND		might get lost (downstream of altered splice site)
388	388	DISULFID	By similarity.	might get lost (downstream of altered splice site)
391	394	STRAND		might get lost (downstream of altered splice site)
395	406	HELIX		might get lost (downstream of altered splice site)
401	401	METAL	Zinc 2; catalytic.	might get lost (downstream of altered splice site)
402	402	ACT_SITE		might get lost (downstream of altered splice site)
402	402	MUTAGEN	E->Q: Loss of activity.	might get lost (downstream of altered splice site)
405	405	METAL	Zinc 2; catalytic.	might get lost (downstream of altered splice site)
411	411	METAL	Zinc 2; catalytic.	might get lost (downstream of altered splice site)
420	422	STRAND		might get lost (downstream of altered splice site)
433	442	HELIX		might get lost (downstream of altered splice site)
515	517	HELIX		might get lost (downstream of altered splice site)
516	516	DISULFID		might get lost (downstream of altered splice site)
521	565	DOMAIN	Hemopexin-like 1.	might get lost (downstream of altered splice site)
522	527	STRAND		might get lost (downstream of altered splice site)
530	535	STRAND		might get lost (downstream of altered splice site)
538	542	STRAND		might get lost (downstream of altered splice site)
545	547	STRAND		might get lost (downstream of altered splice site)
551	555	STRAND		might get lost (downstream of altered splice site)
556	559	HELIX		might get lost (downstream of altered splice site)
567	608	DOMAIN	Hemopexin-like 2.	might get lost (downstream of altered splice site)
568	572	STRAND		might get lost (downstream of altered splice site)
574	576	TURN		might get lost (downstream of altered splice site)
579	583	STRAND		might get lost (downstream of altered splice site)
586	591	STRAND		might get lost (downstream of altered splice site)
594	600	STRAND		might get lost (downstream of altered splice site)
601	604	HELIX		might get lost (downstream of altered splice site)
613	659	DOMAIN	Hemopexin-like 3.	might get lost (downstream of altered splice site)
615	618	STRAND		might get lost (downstream of altered splice site)
623	628	STRAND		might get lost (downstream of altered splice site)
631	636	STRAND		might get lost (downstream of altered splice site)
637	640	TURN		might get lost (downstream of altered splice site)
644	646	HELIX		might get lost (downstream of altered splice site)
650	653	HELIX		might get lost (downstream of altered splice site)
661	704	DOMAIN	Hemopexin-like 4.	might get lost (downstream of altered splice site)
662	667	STRAND		might get lost (downstream of altered splice site)
670	675	STRAND		might get lost (downstream of altered splice site)
678	683	STRAND		might get lost (downstream of altered splice site)
690	696	STRAND		might get lost (downstream of altered splice site)
697	700	TURN		might get lost (downstream of altered splice site)
704	704	DISULFID		might get lost (downstream of altered splice site)
707	707	PROPEP	Removed in 64 kDa matrix metalloproteinase-9 and 67 kDa matrix metalloproteinase-9. /FTId=PRO_0000028757. - EXACT POSITION UNKNOWN	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2124 / 2124

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

708 / 708

position of stopcodon in wt / mu cDNA

2143 / 2143

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

20 / 20

chromosome

strand

last intron/exon boundary

2025

theoretical NMD boundary in CDS

1955

length of CDS

2124

coding sequence (CDS) position

836

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

855

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

2679

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

44640225

original gDNA sequence snippet

CGCCCCAGGACTCTACACCCAGGACGGCAATGCTGATGGGA

altered gDNA sequence snippet

CGCCCCAGGACTCTACACCCGGGACGGCAATGCTGATGGGA

original cDNA sequence snippet

CAGCGAGAGACTCTACACCCAGGACGGCAATGCTGATGGGA

altered cDNA sequence snippet

CAGCGAGAGACTCTACACCCGGGACGGCAATGCTGATGGGA

wildtype AA sequence

MSLWQPLVLV LLVLGCCFAA PRQRQSTLVL FPGDLRTNLT DRQLAEEYLY RYGYTRVAEM
RGESKSLGPA LLLLQKQLSL PETGELDSAT LKAMRTPRCG VPDLGRFQTF EGDLKWHHHN
ITYWIQNYSE DLPRAVIDDA FARAFALWSA VTPLTFTRVY SRDADIVIQF GVAEHGDGYP
FDGKDGLLAH AFPPGPGIQG DAHFDDDELW SLGKGVVVPT RFGNADGAAC HFPFIFEGRS
YSACTTDGRS DGLPWCSTTA NYDTDDRFGF CPSERLYTQD GNADGKPCQF PFIFQGQSYS
ACTTDGRSDG YRWCATTANY DRDKLFGFCP TRADSTVMGG NSAGELCVFP FTFLGKEYST
CTSEGRGDGR LWCATTSNFD SDKKWGFCPD QGYSLFLVAA HEFGHALGLD HSSVPEALMY
PMYRFTEGPP LHKDDVNGIR HLYGPRPEPE PRPPTTTTPQ PTAPPTVCPT GPPTVHPSER
PTAGPTGPPS AGPTGPPTAG PSTATTVPLS PVDDACNVNI FDAIAEIGNQ LYLFKDGKYW
RFSEGRGSRP QGPFLIADKW PALPRKLDSV FEERLSKKLF FFSGRQVWVY TGASVLGPRR
LDKLGLGADV AQVTGALRSG RGKMLLFSGR RLWRFDVKAQ MVDPRSASEV DRMFPGVPLD
THDVFQYREK AYFCQDRFYW RVSSRSELNQ VDQVGYVTYD ILQCPED*

mutated AA sequence

MSLWQPLVLV LLVLGCCFAA PRQRQSTLVL FPGDLRTNLT DRQLAEEYLY RYGYTRVAEM
RGESKSLGPA LLLLQKQLSL PETGELDSAT LKAMRTPRCG VPDLGRFQTF EGDLKWHHHN
ITYWIQNYSE DLPRAVIDDA FARAFALWSA VTPLTFTRVY SRDADIVIQF GVAEHGDGYP
FDGKDGLLAH AFPPGPGIQG DAHFDDDELW SLGKGVVVPT RFGNADGAAC HFPFIFEGRS
YSACTTDGRS DGLPWCSTTA NYDTDDRFGF CPSERLYTRD GNADGKPCQF PFIFQGQSYS
ACTTDGRSDG YRWCATTANY DRDKLFGFCP TRADSTVMGG NSAGELCVFP FTFLGKEYST
CTSEGRGDGR LWCATTSNFD SDKKWGFCPD QGYSLFLVAA HEFGHALGLD HSSVPEALMY
PMYRFTEGPP LHKDDVNGIR HLYGPRPEPE PRPPTTTTPQ PTAPPTVCPT GPPTVHPSER
PTAGPTGPPS AGPTGPPTAG PSTATTVPLS PVDDACNVNI FDAIAEIGNQ LYLFKDGKYW
RFSEGRGSRP QGPFLIADKW PALPRKLDSV FEERLSKKLF FFSGRQVWVY TGASVLGPRR
LDKLGLGADV AQVTGALRSG RGKMLLFSGR RLWRFDVKAQ MVDPRSASEV DRMFPGVPLD
THDVFQYREK AYFCQDRFYW RVSSRSELNQ VDQVGYVTYD ILQCPED*

speed

0.74 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

polymorphism

Problems