mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999428 (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)

chr14:39818028A>GN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000348007

Genbank transcript ID

NM_001247988

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1966A>G
cDNA.2012A>G
g.83541A>G

AA changes

I656V Score: 29 explain score(s)

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

656

frameshift

known variant

Reference ID: rs1140952

database	homozygous (G/G)	heterozygous	allele carriers
1000G	419	1088	1507
ExAC	9516	13735	23251

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.381	0
	-0.347	0
(flanking)	0.968	0.001

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 marginally increased	83539	wt: 0.8806 / mu: 0.9021 (marginal change - not scored)	wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC	ctcc\|AATC
Acc increased	83540	wt: 0.68 / mu: 0.87	wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC	tcca\|ATCA
Acc marginally increased	83534	wt: 0.9483 / mu: 0.9585 (marginal change - not scored)	wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT	tctt\|GCTC
Acc marginally increased	83535	wt: 0.9069 / mu: 0.9174 (marginal change - not scored)	wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG	cttg\|CTCC
Acc increased	83532	wt: 0.36 / mu: 0.53	wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA	cctc\|TTGC
Acc marginally increased	83531	wt: 0.9921 / mu: 0.9928 (marginal change - not scored)	wt: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCC mu: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCC	acct\|CTTG
Acc increased	83533	wt: 0.70 / mu: 0.86	wt: TGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCAT mu: TGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCAT	ctct\|TGCT
Donor gained	83540	0.85	mu: GCTCCAGTCAGAGGT	TCCA\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

656

mutated

all conserved

656

Ptroglodytes

all identical

ENSPTRG00000006297

699

Mmulatta

all identical

ENSMMUG00000021121

700

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000021000

701

Ggallus

all conserved

ENSGALG00000010189

1220

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000023516

596

Dmelanogaster

all conserved

FBgn0031842

1290

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
678	678	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2286 / 2286

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

762 / 762

position of stopcodon in wt / mu cDNA

2332 / 2332

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

47 / 47

chromosome

strand

last intron/exon boundary

2166

theoretical NMD boundary in CDS

2069

length of CDS

2286

coding sequence (CDS) position

1966

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

2012

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

83541

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

39818028

original gDNA sequence snippet

TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA

altered gDNA sequence snippet

TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA

original cDNA sequence snippet

TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA

altered cDNA sequence snippet

TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA

wildtype AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPIRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPGDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*

mutated AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPVRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPGDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*

speed

1.25 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