mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999821 (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)

chr2:1460004G>TN/A show variant in all transcripts IGV

HGNC symbol

TPO

Ensembl transcript ID

ENST00000382201

Genbank transcript ID

NM_001206745

UniProt peptide

P07202

alteration type

single base exchange

alteration region

CDS

DNA changes

c.769G>T
cDNA.841G>T
g.82010G>T

AA changes

A257S Score: 99 explain score(s)

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

257

frameshift

known variant

Reference ID: rs4927611

database	homozygous (T/T)	heterozygous	allele carriers
1000G	374	1082	1456
ExAC	8919	14929	23848

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.824	0
	-0.01	0
(flanking)	0.196	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	82003	0.32	mu: TTCGGGGGAGGGTCT	CGGG\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

257

mutated

all conserved

257

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000009662

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000020673

251

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000033280

n/a

Dmelanogaster

no homologue

Celegans

all identical

K09C8.5

775

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
19	846	TOPO_DOM	Extracellular (Potential).	lost
259	259	DISULFID	By similarity.	might get lost (downstream of altered splice site)
263	263	DISULFID	By similarity.	might get lost (downstream of altered splice site)
269	269	DISULFID	By similarity.	might get lost (downstream of altered splice site)
286	286	DISULFID	By similarity.	might get lost (downstream of altered splice site)
307	307	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
321	321	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
323	323	METAL	Calcium; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
325	325	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
327	327	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
342	342	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
354	354	CONFLICT	A -> G (in Ref. 5 and 8).	might get lost (downstream of altered splice site)
371	371	CONFLICT	A -> R (in Ref. 1; AAA61215/AAA61216).	might get lost (downstream of altered splice site)
381	381	CONFLICT	I -> N (in Ref. 5 and 8).	might get lost (downstream of altered splice site)
396	396	SITE	Transition state stabilizer (By similarity).	might get lost (downstream of altered splice site)
399	399	BINDING	Heme (covalent; via 2 links) (By similarity).	might get lost (downstream of altered splice site)
494	494	METAL	Iron (heme axial ligand) (By similarity).	might get lost (downstream of altered splice site)
569	569	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
574	574	CONFLICT	D -> N (in Ref. 2; CAA68467).	might get lost (downstream of altered splice site)
598	598	DISULFID	By similarity.	might get lost (downstream of altered splice site)
655	655	DISULFID	By similarity.	might get lost (downstream of altered splice site)
696	696	DISULFID	By similarity.	might get lost (downstream of altered splice site)
721	721	DISULFID	By similarity.	might get lost (downstream of altered splice site)
732	732	CONFLICT	W -> C (in Ref. 7; AAN11302).	might get lost (downstream of altered splice site)
740	795	DOMAIN	Sushi.	might get lost (downstream of altered splice site)
748	748	CONFLICT	V -> M (in Ref. 2 and 7).	might get lost (downstream of altered splice site)
796	839	DOMAIN	EGF-like; calcium-binding (Potential).	might get lost (downstream of altered splice site)
800	800	DISULFID	By similarity.	might get lost (downstream of altered splice site)
808	808	DISULFID	By similarity.	might get lost (downstream of altered splice site)
814	814	DISULFID	By similarity.	might get lost (downstream of altered splice site)
816	816	CONFLICT	N -> S (in Ref. 6; AAL74416).	might get lost (downstream of altered splice site)
823	823	DISULFID	By similarity.	might get lost (downstream of altered splice site)
825	825	DISULFID	By similarity.	might get lost (downstream of altered splice site)
838	838	DISULFID	By similarity.	might get lost (downstream of altered splice site)
847	871	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
872	872	CONFLICT	R -> K (in Ref. 2 and 7).	might get lost (downstream of altered splice site)
872	933	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2631 / 2631

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

877 / 877

position of stopcodon in wt / mu cDNA

2703 / 2703

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

73 / 73

chromosome

strand

last intron/exon boundary

2650

theoretical NMD boundary in CDS

2527

length of CDS

2631

coding sequence (CDS) position

769

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

841

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

82010

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

1460004

original gDNA sequence snippet

AAGCTGCCTTCGGGGGAGGGGCTGACTGCCAGATGACTTGT

altered gDNA sequence snippet

AAGCTGCCTTCGGGGGAGGGTCTGACTGCCAGATGACTTGT

original cDNA sequence snippet

AAGCTGCCTTCGGGGGAGGGGCTGACTGCCAGATGACTTGT

altered cDNA sequence snippet

AAGCTGCCTTCGGGGGAGGGTCTGACTGCCAGATGACTTGT

wildtype AA sequence

MRALAVLSVT LVMACTEAFF PFISRGKELL WGKPEESRVS SVLEESKRLV DTAMYATMQR
NLKKRGILSP AQLLSFSKLP EPTSGVIARA AEIMETSIQA MKRKVNLKTQ QSQHPTDALS
EDLLSIIANM SGCLPYMLPP KCPNTCLANK YRPITGACNN RDHPRWGASN TALARWLPPV
YEDGFSQPRG WNPGFLYNGF PLPPVREVTR HVIQVSNEVV TDDDRYSDLL MAWGQYIDHD
IAFTPQSTSK AAFGGGADCQ MTCENQNPCF PIQLPEEARP AAGTACLPFY RSSAACGTGD
QGALFGNLST ANPRQQMNGL TSFLDASTVY GSSPALERQL RNWTSAEGLL RVHARLRDSG
RAYLPFVPPR APAACAPEPG IPGETRGPCF LAGDGRASEV PSLTALHTLW LREHNRLAAA
LKALNAHWSA DAVYQEARKV VGALHQIITL RDYIPRILGP EAFQQYVGPY EGYDSTANPT
VSNVFSTAAF RFGHATIHPL VRRLDASFQE HPDLPGLWLH QAFFSPWTLL RGGYNEWREF
CGLPRLETPA DLSTAIASRS VADKILDLYK HPDNIDVWLG GLAENFLPRA RTGPLFACLI
GKQMKALRDG DWFWWENSHV FTDAQRRELE KHSLSRVICD NTGLTRVPMD AFQVGKFPED
FESCDSITGM NLEAWRETFP QDDKCGFPES VENGDFVHCE ESGRRVLVYS CRHGYELQGR
EQLTCTQEGW DFQPPLCKDV NECADGAHPP CHASARCRNT KGGFQCLCAD PYELGDDGRT
CVDSGRLPRV TWISMSLAAL LIGGFAGLTS TVICRWTRTG TKSTLPISET GGGTPELRCG
KHQAVGTSPQ RAAAQDSEQE SAGMEGRDTH RLPRAL*

mutated AA sequence

MRALAVLSVT LVMACTEAFF PFISRGKELL WGKPEESRVS SVLEESKRLV DTAMYATMQR
NLKKRGILSP AQLLSFSKLP EPTSGVIARA AEIMETSIQA MKRKVNLKTQ QSQHPTDALS
EDLLSIIANM SGCLPYMLPP KCPNTCLANK YRPITGACNN RDHPRWGASN TALARWLPPV
YEDGFSQPRG WNPGFLYNGF PLPPVREVTR HVIQVSNEVV TDDDRYSDLL MAWGQYIDHD
IAFTPQSTSK AAFGGGSDCQ MTCENQNPCF PIQLPEEARP AAGTACLPFY RSSAACGTGD
QGALFGNLST ANPRQQMNGL TSFLDASTVY GSSPALERQL RNWTSAEGLL RVHARLRDSG
RAYLPFVPPR APAACAPEPG IPGETRGPCF LAGDGRASEV PSLTALHTLW LREHNRLAAA
LKALNAHWSA DAVYQEARKV VGALHQIITL RDYIPRILGP EAFQQYVGPY EGYDSTANPT
VSNVFSTAAF RFGHATIHPL VRRLDASFQE HPDLPGLWLH QAFFSPWTLL RGGYNEWREF
CGLPRLETPA DLSTAIASRS VADKILDLYK HPDNIDVWLG GLAENFLPRA RTGPLFACLI
GKQMKALRDG DWFWWENSHV FTDAQRRELE KHSLSRVICD NTGLTRVPMD AFQVGKFPED
FESCDSITGM NLEAWRETFP QDDKCGFPES VENGDFVHCE ESGRRVLVYS CRHGYELQGR
EQLTCTQEGW DFQPPLCKDV NECADGAHPP CHASARCRNT KGGFQCLCAD PYELGDDGRT
CVDSGRLPRV TWISMSLAAL LIGGFAGLTS TVICRWTRTG TKSTLPISET GGGTPELRCG
KHQAVGTSPQ RAAAQDSEQE SAGMEGRDTH RLPRAL*

speed

0.84 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