mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999988091858901 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:130374102C>AN/A show variant in all transcripts IGV

HGNC symbol

L3MBTL3

Ensembl transcript ID

ENST00000526019

Genbank transcript ID

N/A

UniProt peptide

Q96JM7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.473C>A
cDNA.716C>A
g.39259C>A

AA changes

T158N Score: 65 explain score(s)

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

158

frameshift

known variant

Reference ID: rs9388768

database	homozygous (A/A)	heterozygous	allele carriers
1000G	777	970	1747
ExAC	25084	-17401	7683

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.973	0.042
	2.059	0.939
(flanking)	0.775	0.977

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	39261	wt: 0.50 / mu: 0.61	wt: ACACCAAGGAGGATG mu: ACAACAAGGAGGATG	ACCA\|agga
Donor increased	39251	wt: 0.35 / mu: 0.39	wt: CTGAAAGCTGACACC mu: CTGAAAGCTGACAAC	GAAA\|gctg
Donor increased	39262	wt: 0.24 / mu: 0.29	wt: CACCAAGGAGGATGG mu: CAACAAGGAGGATGG	CCAA\|ggag
Donor increased	39254	wt: 0.34 / mu: 0.84	wt: AAAGCTGACACCAAG mu: AAAGCTGACAACAAG	AGCT\|gaca
Donor gained	39263	0.31	mu: AACAAGGAGGATGGA	CAAG\|gagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

158

mutated

not conserved

158

Ptroglodytes

not conserved

ENSPTRG00000023858

Mmulatta

not conserved

ENSMMUG00000021498

183

Fcatus

all conserved

ENSFCAG00000001466

183

Mmusculus

all conserved

ENSMUSG00000039089

183

Ggallus

all conserved

ENSGALG00000014009

186

ENP

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000025983

114

SMDIP

Dmelanogaster

all identical

FBgn0002441

782

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
232	332	REPEAT	MBT 1.	might get lost (downstream of altered splice site)
234	241	HELIX		might get lost (downstream of altered splice site)
248	250	HELIX		might get lost (downstream of altered splice site)
253	255	TURN		might get lost (downstream of altered splice site)
269	274	STRAND		might get lost (downstream of altered splice site)
277	290	STRAND		might get lost (downstream of altered splice site)
293	298	STRAND		might get lost (downstream of altered splice site)
303	305	HELIX		might get lost (downstream of altered splice site)
307	310	STRAND		might get lost (downstream of altered splice site)
314	317	STRAND		might get lost (downstream of altered splice site)
321	325	HELIX		might get lost (downstream of altered splice site)
337	339	TURN		might get lost (downstream of altered splice site)
340	439	REPEAT	MBT 2.	might get lost (downstream of altered splice site)
342	348	HELIX		might get lost (downstream of altered splice site)
356	358	HELIX		might get lost (downstream of altered splice site)
360	363	TURN		might get lost (downstream of altered splice site)
376	381	STRAND		might get lost (downstream of altered splice site)
384	397	STRAND		might get lost (downstream of altered splice site)
400	405	STRAND		might get lost (downstream of altered splice site)
410	412	HELIX		might get lost (downstream of altered splice site)
414	416	STRAND		might get lost (downstream of altered splice site)
428	431	HELIX		might get lost (downstream of altered splice site)
448	543	REPEAT	MBT 3.	might get lost (downstream of altered splice site)
450	456	HELIX		might get lost (downstream of altered splice site)
464	466	HELIX		might get lost (downstream of altered splice site)
472	474	STRAND		might get lost (downstream of altered splice site)
480	484	STRAND		might get lost (downstream of altered splice site)
486	488	STRAND		might get lost (downstream of altered splice site)
492	500	STRAND		might get lost (downstream of altered splice site)
502	509	STRAND		might get lost (downstream of altered splice site)
510	512	STRAND		might get lost (downstream of altered splice site)
514	516	HELIX		might get lost (downstream of altered splice site)
518	521	STRAND		might get lost (downstream of altered splice site)
532	536	HELIX		might get lost (downstream of altered splice site)
546	549	TURN		might get lost (downstream of altered splice site)
608	608	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
708	772	DOMAIN	SAM.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2268 / 2268

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

756 / 756

position of stopcodon in wt / mu cDNA

2511 / 2511

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

244 / 244

chromosome

strand

last intron/exon boundary

2368

theoretical NMD boundary in CDS

2074

length of CDS

2268

coding sequence (CDS) position

473

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

716

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

39259

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

130374102

original gDNA sequence snippet

ATTATCTCTGAAAGCTGACACCAAGGAGGATGGAGAAGAGA

altered gDNA sequence snippet

ATTATCTCTGAAAGCTGACAACAAGGAGGATGGAGAAGAGA

original cDNA sequence snippet

ATTATCTCTGAAAGCTGACACCAAGGAGGATGGAGAAGAGA

altered cDNA sequence snippet

ATTATCTCTGAAAGCTGACAACAAGGAGGATGGAGAAGAGA

wildtype AA sequence

MTESASSTSG QEFDVFSVMD WKDGVGTLPG SDLKFRVNEF GALEVITDEN EMENVKKATA
TTTWMVPTAQ EVFSEKTGMP FRLKDPVKVE GLQFCENCCQ YGNVDECLSG GNYCSQNCAR
HIKDKDQKEE RDVEEDNEEE DPKCSRKKKP KLSLKADTKE DGEERDDEME NKQDVRILRG
SQRARRKRRG DSAVLKQGLP PKGKKAWCWA SYLEEEKAVA VPAKLFKEHQ SFPYNKNGFK
VGMKLEGVDP EHQSVYCVLT VAEVCGYRIK LHFDGYSDCY DFWVNADALD IHPVGWCEKT
GHKLHPPKGY KEEEFNWQTY LKTCKAQAAP KSLFENQNIT VIPSGFRVGM KLEAVDKKNP
SFICVATVTD MVDNRFLVHF DNWDESYDYW CEASSPHIHP VGWCKEHRRT LITPPGYPNV
KHFSWDKYLE ETNSLPAPAR AFKVKPPHGF QKKMKLEVVD KRNPMFIRVA TVADTDDHRV
KVHFDGWNNC YDYWIDADSP DIHPVGWCSK TGHPLQPPLS PLELMEASEH GGCSTPGCKG
IGHFKRARHL GPHSAANCPY SEINLNKDRI FPDRLSGEMP PASPSFPRNK RTDANESSSS
PEIRDQHADD VKEDFEERTE SEMRTSHEAR GAREEPTVQQ AQRRSAVFLS FKSPIPCLPL
RWEQQSKLLP TVAGIPASKV SKWSTDEVSE FIQSLPGCEE HGKVFKDEQI DGEAFLLMTQ
TDIVKIMSIK LGPALKIFNS ILMFKAAEKN SHNEL*

mutated AA sequence

MTESASSTSG QEFDVFSVMD WKDGVGTLPG SDLKFRVNEF GALEVITDEN EMENVKKATA
TTTWMVPTAQ EVFSEKTGMP FRLKDPVKVE GLQFCENCCQ YGNVDECLSG GNYCSQNCAR
HIKDKDQKEE RDVEEDNEEE DPKCSRKKKP KLSLKADNKE DGEERDDEME NKQDVRILRG
SQRARRKRRG DSAVLKQGLP PKGKKAWCWA SYLEEEKAVA VPAKLFKEHQ SFPYNKNGFK
VGMKLEGVDP EHQSVYCVLT VAEVCGYRIK LHFDGYSDCY DFWVNADALD IHPVGWCEKT
GHKLHPPKGY KEEEFNWQTY LKTCKAQAAP KSLFENQNIT VIPSGFRVGM KLEAVDKKNP
SFICVATVTD MVDNRFLVHF DNWDESYDYW CEASSPHIHP VGWCKEHRRT LITPPGYPNV
KHFSWDKYLE ETNSLPAPAR AFKVKPPHGF QKKMKLEVVD KRNPMFIRVA TVADTDDHRV
KVHFDGWNNC YDYWIDADSP DIHPVGWCSK TGHPLQPPLS PLELMEASEH GGCSTPGCKG
IGHFKRARHL GPHSAANCPY SEINLNKDRI FPDRLSGEMP PASPSFPRNK RTDANESSSS
PEIRDQHADD VKEDFEERTE SEMRTSHEAR GAREEPTVQQ AQRRSAVFLS FKSPIPCLPL
RWEQQSKLLP TVAGIPASKV SKWSTDEVSE FIQSLPGCEE HGKVFKDEQI DGEAFLLMTQ
TDIVKIMSIK LGPALKIFNS ILMFKAAEKN SHNEL*

speed

1.14 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