mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999848 (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

ENST00000341749

Genbank transcript ID

NM_203354

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2059A>G
cDNA.2162A>G
g.83541A>G

AA changes

I687V Score: 29 explain score(s)

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

687

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

687

mutated

all conserved

687

Ptroglodytes

all identical

ENSPTRG00000006297

699

Mmulatta

all identical

ENSMMUG00000021121

700

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000021000

701

Ggallus

all conserved

ENSGALG00000010189

1221

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000023516

600

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
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

2379 / 2379

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

793 / 793

position of stopcodon in wt / mu cDNA

2482 / 2482

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

104 / 104

chromosome

strand

last intron/exon boundary

2316

theoretical NMD boundary in CDS

2162

length of CDS

2379

coding sequence (CDS) position

2059

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

2162

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

MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*

mutated AA sequence

MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPVRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*

speed

1.32 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