mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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)

chr12:25671759T>AN/A show variant in all transcripts IGV

HGNC symbol

LMNTD1

Ensembl transcript ID

ENST00000413632

Genbank transcript ID

NM_001145729

UniProt peptide

Q8N9Z9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1039A>T
cDNA.1282A>T
g.129755A>T

AA changes

T347S Score: 58 explain score(s)

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

347

frameshift

known variant

Reference ID: rs1479500

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1324	932	2256
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.404	0.001
	-0.995	0
(flanking)	0.102	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 gained	129748	0.92	mu: AGACAGCCCAGGTCT	ACAG\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

347

mutated

all conserved

347

Ptroglodytes

all conserved

ENSPTRG00000004776

387

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000054966

395

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
381	381	CONFLICT	K -> E (in Ref. 1; BAG59389).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1110 / 1110

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

370 / 370

position of stopcodon in wt / mu cDNA

1353 / 1353

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

-1

last intron/exon boundary

1376

theoretical NMD boundary in CDS

1082

length of CDS

1110

coding sequence (CDS) position

1039

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

1282

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

129755

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

25671759

original gDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered gDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

original cDNA sequence snippet

GATTGGATAGACAGCCCAGGACTCGGTCAACCAGACCTAAT

altered cDNA sequence snippet

GATTGGATAGACAGCCCAGGTCTCGGTCAACCAGACCTAAT

wildtype AA sequence

MKDTQDIQEA SKAMQNKVHE QEDKNEKQKQ REDKLGVYSL VHFSPKMLGS VATTLPLSSS
NSSGMPLGYY LSSPQISRVT ISTTGQLTSK ATVGSCSRVE NSLDASPFSV PKKQDESPMI
GDGEDYFLSL FGDSKKLTAH SNYTQKTLKY FSMILEEVGQ FTSSSLGDVE IAEVNVKGLF
VKLINSSLDK EMAIGDHILQ QNVNGQTISL YRFLPNIVMQ ANSTVTAIAW YTPIHWKQAW
EKLDADVEFN RCSVVSPTFR KRVFQWTAST ATITKEKQDQ PKKDISNYQV EQAQVLLKRE
KEIPPTVFPN RSPWCQNPYV SAHPYCPLIE PHNTSTAGGR LDRQPRTRST RPNRASGSKK
KKTSESQKQ*

mutated AA sequence

speed

1.07 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