mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999671 (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)

chr11:114401611A>GN/A show variant in all transcripts IGV

HGNC symbol

NXPE1

Ensembl transcript ID

ENST00000536312

Genbank transcript ID

N/A

UniProt peptide

Q8N323

alteration type

single base exchange

alteration region

CDS

DNA changes

c.119T>C
cDNA.1012T>C
g.29007T>C

AA changes

L40S Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs7944960

database	homozygous (G/G)	heterozygous	allele carriers
1000G	240	716	956
ExAC	2328	15532	17860

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.078	0.002
	0.231	0.001
(flanking)	-1.563	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
Acc increased	29001	wt: 0.23 / mu: 0.29	wt: ATTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCC mu: ATTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCC	ctct\|AAAC
Acc increased	29002	wt: 0.52 / mu: 0.58	wt: TTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCA mu: TTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCA	tcta\|AACT
Donor gained	28999	0.37	mu: TCTGCTCTAAACTCA	TGCT\|ctaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no alignment

ENSPTRG00000004307

n/a

Mmulatta

no alignment

ENSMMUG00000012268

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000003928

n/a

protein features

start (aa)	end (aa)	feature	details
39	39	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
211	211	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
491	491	CONFLICT	G -> V (in Ref. 4; AAH29049).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

888 / 888

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

296 / 296

position of stopcodon in wt / mu cDNA

1781 / 1781

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

894 / 894

chromosome

strand

-1

last intron/exon boundary

1826

theoretical NMD boundary in CDS

882

length of CDS

888

coding sequence (CDS) position

119

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

1012

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

29007

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

114401611

original gDNA sequence snippet

GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT

altered gDNA sequence snippet

GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT

original cDNA sequence snippet

GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT

altered cDNA sequence snippet

GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT

wildtype AA sequence

MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNL SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRMA PGETSIAGNQ VQSGS*

mutated AA sequence

MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNS SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRMA PGETSIAGNQ VQSGS*

speed

0.78 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