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: ENST00000265081
MT speed 0 s - this script 3.020647 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MSH3	polymorphism_automatic	1.49880108324396e-11	simple_aae		affected		A1045T	single base exchange	rs26279		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999985012 (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 CM076321)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:80168937G>AN/A show variant in all transcripts IGV

HGNC symbol

MSH3

Ensembl transcript ID

ENST00000265081

Genbank transcript ID

NM_002439

UniProt peptide

P20585

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3133G>A
cDNA.3213G>A
g.218471G>A

AA changes

A1045T Score: 58 explain score(s)

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

1045

frameshift

known variant

Reference ID: rs26279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1305	997	2302
ExAC	32457	-32147	310

known disease mutation at this position, please check HGMD for details (HGMD ID CM076321)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.014	0.058
	-0.687	0.002
(flanking)	1.119	0.173

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	218468	sequence motif lost	-	wt: acag\|GCGC mu: acag.GCAC
Acc marginally increased	218462	wt: 0.7645 / mu: 0.8356 (marginal change - not scored)	wt: TTTTGATCTCCTTTCTTTATTTCACAGGCGCAGCAGAACAA mu: TTTTGATCTCCTTTCTTTATTTCACAGGCACAGCAGAACAA	tatt\|TCAC
Acc marginally decreased	218468	wt: 0.9906 / mu: 0.9902 (marginal change - not scored)	wt: TCTCCTTTCTTTATTTCACAGGCGCAGCAGAACAAGTCCCT mu: TCTCCTTTCTTTATTTCACAGGCACAGCAGAACAAGTCCCT	acag\|GCGC
Donor increased	218473	wt: 0.77 / mu: 0.95	wt: GGCGCAGCAGAACAA mu: GGCACAGCAGAACAA	CGCA\|gcag
Donor increased	218467	wt: 0.55 / mu: 0.91	wt: TTCACAGGCGCAGCA mu: TTCACAGGCACAGCA	CACA\|ggcg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1045

mutated

not conserved

1045

Ptroglodytes

all identical

ENSPTRG00000017043

1039

Mmulatta

not conserved

ENSMMUG00000018284

1032

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000014850

1003

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1055	1062	STRAND		might get lost (downstream of altered splice site)
1066	1069	TURN		might get lost (downstream of altered splice site)
1068	1068	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
1070	1073	HELIX		might get lost (downstream of altered splice site)
1074	1077	TURN		might get lost (downstream of altered splice site)
1080	1111	HELIX		might get lost (downstream of altered splice site)
1116	1128	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3414 / 3414

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

1138 / 1138

position of stopcodon in wt / mu cDNA

3494 / 3494

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

81 / 81

chromosome

strand

last intron/exon boundary

3383

theoretical NMD boundary in CDS

3252

length of CDS

3414

coding sequence (CDS) position

3133

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

3213

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

218471

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

80168937

original gDNA sequence snippet

CCTTTCTTTATTTCACAGGCGCAGCAGAACAAGTCCCTGAT

altered gDNA sequence snippet

CCTTTCTTTATTTCACAGGCACAGCAGAACAAGTCCCTGAT

original cDNA sequence snippet

AAAGCAAACTGGATCCAGGCGCAGCAGAACAAGTCCCTGAT

altered cDNA sequence snippet

AAAGCAAACTGGATCCAGGCACAGCAGAACAAGTCCCTGAT

wildtype AA sequence

MSRRKPASGG LAASSSAPAR QAVLSRFFQS TGSLKSTSSS TGAADQVDPG AAAAAAAAAA
AAPPAPPAPA FPPQLPPHIA TEIDRRKKRP LENDGPVKKK VKKVQQKEGG SDLGMSGNSE
PKKCLRTRNV SKSLEKLKEF CCDSALPQSR VQTESLQERF AVLPKCTDFD DISLLHAKNA
VSSEDSKRQI NQKDTTLFDL SQFGSSNTSH ENLQKTASKS ANKRSKSIYT PLELQYIEMK
QQHKDAVLCV ECGYKYRFFG EDAEIAAREL NIYCHLDHNF MTASIPTHRL FVHVRRLVAK
GYKVGVVKQT ETAALKAIGD NRSSLFSRKL TALYTKSTLI GEDVNPLIKL DDAVNVDEIM
TDTSTSYLLC ISENKENVRD KKKGNIFIGI VGVQPATGEV VFDSFQDSAS RSELETRMSS
LQPVELLLPS ALSEQTEALI HRATSVSVQD DRIRVERMDN IYFEYSHAFQ AVTEFYAKDT
VDIKGSQIIS GIVNLEKPVI CSLAAIIKYL KEFNLEKMLS KPENFKQLSS KMEFMTINGT
TLRNLEILQN QTDMKTKGSL LWVLDHTKTS FGRRKLKKWV TQPLLKLREI NARLDAVSEV
LHSESSVFGQ IENHLRKLPD IERGLCSIYH KKCSTQEFFL IVKTLYHLKS EFQAIIPAVN
SHIQSDLLRT VILEIPELLS PVEHYLKILN EQAAKVGDKT ELFKDLSDFP LIKKRKDEIQ
GVIDEIRMHL QEIRKILKNP SAQYVTVSGQ EFMIEIKNSA VSCIPTDWVK VGSTKAVSRF
HSPFIVENYR HLNQLREQLV LDCSAEWLDF LEKFSEHYHS LCKAVHHLAT VDCIFSLAKV
AKQGDYCRPT VQEERKIVIK NGRHPVIDVL LGEQDQYVPN NTDLSEDSER VMIITGPNMG
GKSSYIKQVA LITIMAQIGS YVPAEEATIG IVDGIFTRMG AADNIYKGQS TFMEELTDTA
EIIRKATSQS LVILDELGRG TSTHDGIAIA YATLEYFIRD VKSLTLFVTH YPPVCELEKN
YSHQVGNYHM GFLVSEDESK LDPGAAEQVP DFVTFLYQIT RGIAARSYGL NVAKLADVPG
EILKKAAHKS KELEGLINTK RKRLKYFAKL WTMHNAQDLQ KWTEEFNMEE TQTSLLH*

mutated AA sequence

MSRRKPASGG LAASSSAPAR QAVLSRFFQS TGSLKSTSSS TGAADQVDPG AAAAAAAAAA
AAPPAPPAPA FPPQLPPHIA TEIDRRKKRP LENDGPVKKK VKKVQQKEGG SDLGMSGNSE
PKKCLRTRNV SKSLEKLKEF CCDSALPQSR VQTESLQERF AVLPKCTDFD DISLLHAKNA
VSSEDSKRQI NQKDTTLFDL SQFGSSNTSH ENLQKTASKS ANKRSKSIYT PLELQYIEMK
QQHKDAVLCV ECGYKYRFFG EDAEIAAREL NIYCHLDHNF MTASIPTHRL FVHVRRLVAK
GYKVGVVKQT ETAALKAIGD NRSSLFSRKL TALYTKSTLI GEDVNPLIKL DDAVNVDEIM
TDTSTSYLLC ISENKENVRD KKKGNIFIGI VGVQPATGEV VFDSFQDSAS RSELETRMSS
LQPVELLLPS ALSEQTEALI HRATSVSVQD DRIRVERMDN IYFEYSHAFQ AVTEFYAKDT
VDIKGSQIIS GIVNLEKPVI CSLAAIIKYL KEFNLEKMLS KPENFKQLSS KMEFMTINGT
TLRNLEILQN QTDMKTKGSL LWVLDHTKTS FGRRKLKKWV TQPLLKLREI NARLDAVSEV
LHSESSVFGQ IENHLRKLPD IERGLCSIYH KKCSTQEFFL IVKTLYHLKS EFQAIIPAVN
SHIQSDLLRT VILEIPELLS PVEHYLKILN EQAAKVGDKT ELFKDLSDFP LIKKRKDEIQ
GVIDEIRMHL QEIRKILKNP SAQYVTVSGQ EFMIEIKNSA VSCIPTDWVK VGSTKAVSRF
HSPFIVENYR HLNQLREQLV LDCSAEWLDF LEKFSEHYHS LCKAVHHLAT VDCIFSLAKV
AKQGDYCRPT VQEERKIVIK NGRHPVIDVL LGEQDQYVPN NTDLSEDSER VMIITGPNMG
GKSSYIKQVA LITIMAQIGS YVPAEEATIG IVDGIFTRMG AADNIYKGQS TFMEELTDTA
EIIRKATSQS LVILDELGRG TSTHDGIAIA YATLEYFIRD VKSLTLFVTH YPPVCELEKN
YSHQVGNYHM GFLVSEDESK LDPGTAEQVP DFVTFLYQIT RGIAARSYGL NVAKLADVPG
EILKKAAHKS KELEGLINTK RKRLKYFAKL WTMHNAQDLQ KWTEEFNMEE TQTSLLH*

speed

0.91 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