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: ENST00000472487
MT speed 0.18 s - this script 2.233303 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MYSM1	polymorphism_automatic	3.369240442197e-10	simple_aae		affected		E825K	single base exchange	rs232777		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999663076 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:59125683C>TN/A show variant in all transcripts IGV

HGNC symbol

MYSM1

Ensembl transcript ID

ENST00000472487

Genbank transcript ID

NM_001085487

UniProt peptide

Q5VVJ2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2473G>A
cDNA.2513G>A
g.40082G>A

AA changes

E825K Score: 56 explain score(s)

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

825

frameshift

known variant

Reference ID: rs232777

database	homozygous (T/T)	heterozygous	allele carriers
1000G	244	1027	1271
ExAC	3611	20996	24607

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.979	0.014
	0.067	0.001
(flanking)	-0.032	0

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
Donor increased	40086	wt: 0.21 / mu: 0.39	wt: GGAATTGTTAATGTG mu: GAAATTGTTAATGTG	AATT\|gtta
Donor increased	40087	wt: 0.53 / mu: 0.77	wt: GAATTGTTAATGTGA mu: AAATTGTTAATGTGA	ATTG\|ttaa
Donor increased	40075	wt: 0.80 / mu: 0.88	wt: AACTGTACAAAGGAA mu: AACTGTACAAAGAAA	CTGT\|acaa
Donor marginally increased	40079	wt: 0.6492 / mu: 0.6667 (marginal change - not scored)	wt: GTACAAAGGAATTGT mu: GTACAAAGAAATTGT	ACAA\|agga
Donor gained	40078	0.62	mu: TGTACAAAGAAATTG	TACA\|aaga

distance from splice site

145

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

825

mutated

all conserved

825

Ptroglodytes

all identical

ENSPTRG00000000796

825

Mmulatta

all identical

ENSMMUG00000011800

825

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000062627

816

Ggallus

no alignment

ENSGALG00000010869

n/a

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000034693

765

HLY

Dmelanogaster

no alignment

FBgn0032348

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000011126

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2487 / 2487

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

829 / 829

position of stopcodon in wt / mu cDNA

2527 / 2527

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

41 / 41

chromosome

strand

-1

last intron/exon boundary

2369

theoretical NMD boundary in CDS

2278

length of CDS

2487

coding sequence (CDS) position

2473

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

2513

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

40082

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

59125683

original gDNA sequence snippet

CCGAAGAGAACTGTACAAAGGAATTGTTAATGTGATTATTT

altered gDNA sequence snippet

CCGAAGAGAACTGTACAAAGAAATTGTTAATGTGATTATTT

original cDNA sequence snippet

CCGAAGAGAACTGTACAAAGGAATTGTTAATGTGATTATTT

altered cDNA sequence snippet

CCGAAGAGAACTGTACAAAGAAATTGTTAATGTGATTATTT

wildtype AA sequence

MAAEEADVDI EGDVVAAAGA QPGSGENTAS VLQKDHYLDS SWRTENGLIP WTLDNTISEE
NRAVIEKMLL EEEYYLSKKS QPEKVWLDQK EDDKKYMKSL QKTAKIMVHS PTKPASYSVK
WTIEEKELFE QGLAKFGRRW TKISKLIGSR TVLQVKSYAR QYFKNKVKCG LDKETPNQKT
GHNLQVKNED KGTKAWTPSC LRGRADPNLN AVKIEKLSDD EEVDITDEVD ELSSQTPQKN
SSSDLLLDFP NSKMHETNQG EFITSDSQEA LFSKSSRGCL QNEKQDETLS SSEITLWTEK
QSNGDKKSIE LNDQKFNELI KNCNKHDGRG IIVDARQLPS PEPCEIQKNL NDNEMLFHSC
QMVEESHEEE ELKPPEQEIE IDRNIIQEEE KQAIPEFFEG RQAKTPERYL KIRNYILDQW
EICKPKYLNK TSVRPGLKNC GDVNCIGRIH TYLELIGAIN FGCEQAVYNR PQTVDKVRIR
DRKDAVEAYQ LAQRLQSMRT RRRRVRDPWG NWCDAKDLEG QTFEHLSAEE LAKRREEEKG
RPVKSLKVPR PTKSSFDPFQ LIPCNFFSEE KQEPFQVKVA SEALLIMDLH AHVSMAEVIG
LLGGRYSEVD KVVEVCAAEP CNSLSTGLQC EMDPVSQTQA SETLAVRGFS VIGWYHSHPA
FDPNPSLRDI DTQAKYQSYF SRGGAKFIGM IVSPYNRNNP LPYSQITCLV ISEEISPDGS
YRLPYKFEVQ QMLEEPQWGL VFEKTRWIIE KYRLSHSSVP MDKIFRRDSD LTCLQKLLEC
MRKTLSKVTN CFMAEEFLTE IENLFLSNYK SNQENGVTEE NCTKELLM*

mutated AA sequence

speed

0.18 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