mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999945 (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)

chr7:157931144C>TN/A show variant in all transcripts IGV

HGNC symbol

PTPRN2

Ensembl transcript ID

ENST00000389416

Genbank transcript ID

NM_130842

UniProt peptide

Q92932

alteration type

single base exchange

alteration region

CDS

DNA changes

c.923G>A
cDNA.965G>A
g.449337G>A

AA changes

S308N Score: 46 explain score(s)

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

308

frameshift

known variant

Reference ID: rs1130499

database	homozygous (T/T)	heterozygous	allele carriers
1000G	369	1141	1510
ExAC	7537	17693	25230

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.193	0
	0.414	0.007
(flanking)	0.485	0.015

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 increased	449341	wt: 0.28 / mu: 0.58	wt: AGTGGCCTGGAGCTG mu: AATGGCCTGGAGCTG	TGGC\|ctgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

308

mutated

all conserved

308

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000007989

282

Mmusculus

not conserved

ENSMUSG00000056553

318

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000035970

314

Dmelanogaster

no alignment

FBgn0031294

n/a

Celegans

no alignment

B0244.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
22	615	TOPO_DOM	Extracellular (Potential).	lost
323	323	CONFLICT	G -> R (in Ref. 2; CAA69880).	might get lost (downstream of altered splice site)
427	428	SITE	Cleavage (Potential).	might get lost (downstream of altered splice site)
564	564	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
616	636	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
637	1015	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
692	692	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
725	738	HELIX		might get lost (downstream of altered splice site)
742	754	HELIX		might get lost (downstream of altered splice site)
745	1005	DOMAIN	Tyrosine-protein phosphatase.	might get lost (downstream of altered splice site)
763	766	TURN		might get lost (downstream of altered splice site)
768	770	TURN		might get lost (downstream of altered splice site)
771	773	HELIX		might get lost (downstream of altered splice site)
783	785	HELIX		might get lost (downstream of altered splice site)
791	793	TURN		might get lost (downstream of altered splice site)
795	797	STRAND		might get lost (downstream of altered splice site)
802	806	STRAND		might get lost (downstream of altered splice site)
811	813	STRAND		might get lost (downstream of altered splice site)
815	819	STRAND		might get lost (downstream of altered splice site)
824	826	HELIX		might get lost (downstream of altered splice site)
827	836	HELIX		might get lost (downstream of altered splice site)
841	844	STRAND		might get lost (downstream of altered splice site)
848	850	STRAND		might get lost (downstream of altered splice site)
862	868	STRAND		might get lost (downstream of altered splice site)
871	882	STRAND		might get lost (downstream of altered splice site)
885	894	STRAND		might get lost (downstream of altered splice site)
895	898	TURN		might get lost (downstream of altered splice site)
899	908	STRAND		might get lost (downstream of altered splice site)
913	913	BINDING	Substrate (By similarity).	might get lost (downstream of altered splice site)
920	934	HELIX		might get lost (downstream of altered splice site)
941	944	STRAND		might get lost (downstream of altered splice site)
945	945	ACT_SITE	Phosphocysteine intermediate (By similarity).	might get lost (downstream of altered splice site)
945	945	MUTAGEN	C->S: Loss of activity.	might get lost (downstream of altered splice site)
945	951	REGION	Substrate binding (By similarity).	might get lost (downstream of altered splice site)
946	949	STRAND		might get lost (downstream of altered splice site)
950	966	HELIX		might get lost (downstream of altered splice site)
970	970	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
974	982	HELIX		might get lost (downstream of altered splice site)
977	977	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
990	990	BINDING	Substrate (By similarity).	might get lost (downstream of altered splice site)
992	1010	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2997 / 2997

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

999 / 999

position of stopcodon in wt / mu cDNA

3039 / 3039

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

43 / 43

chromosome

strand

-1

last intron/exon boundary

2968

theoretical NMD boundary in CDS

2875

length of CDS

2997

coding sequence (CDS) position

923

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

965

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

449337

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

157931144

original gDNA sequence snippet

GGCTGAGGTGAGGGGCCTGAGTGGCCTGGAGCTGGACGGCA

altered gDNA sequence snippet

GGCTGAGGTGAGGGGCCTGAATGGCCTGGAGCTGGACGGCA

original cDNA sequence snippet

GGCTGAGGTGAGGGGCCTGAGTGGCCTGGAGCTGGACGGCA

altered cDNA sequence snippet

GGCTGAGGTGAGGGGCCTGAATGGCCTGGAGCTGGACGGCA

wildtype AA sequence

MGPPLPLLLL LLLLLPPRVL PAAPSSVPRG RQLPGRLDGV FGRCQKVPAM DFYRYEVSPV
ALQRLRVALQ KLSGTGFTWQ DDYTQYVMDQ ELADLPKTYL RRPEASSPAR PSKHSVGSER
RYSREGGAAL ANALRRHLPF LEALSQAPAS DVLARTHTAQ DRPPAEGDDR FSESILTYVA
HTSALTYPPG SRTQLREDLL PRTLGQLQPD ELSPKVDSGV DRHHLMAALS AYAAQRPPAP
PGEGSLEPQY LLRAPSRMPR PLLAPAAPQK WPSPLGDSED PSSTGDGARI HTLLKDLQRQ
PAEVRGLSGL ELDGMAELMA GLMQGVDHGV ARGSPGRAAL GESGEQADGP KATLRGDSFP
DDGVQDDDDR LYQEVHRLSA TLGGLLQDHG SRLLPGALPF ARPLDMERKK SEHPESSLSS
EEETAGVENV KSQTYSKDLL GQQPHSEPGA AAFGELQNQM PGPSKEEQSL PAGAQEALSD
GLQLEVQPSE EEARGYIVTD RDPLRPEEGR RLVEDVARLL QVPSSAFADV EVLGPAVTFK
VSANVQNVTT EDVEKATVDN KDKLEETSGL KILQTGVGSK SKLKFLPPQA EQEDSTKFIA
LTLVSLACIL GVLLASGLIY CLRHSSQHRL KEKLSGLGGD PGADATAAYQ ELCRQRMATR
PPDRPEGPHT SRISSVSSQF SDGPIPSPSA RSSASSWSEE PVQSNMDIST GHMILSYMED
HLKNKNRLEK EWEALCAYQA EPNSSFVAQR EENVPKNRSL AVLTYDHSRV LLKAENSHSH
SDYINASPIM DHDPRNPAYI ATQGPLPATV ADFWQMVWES GCVVIVMLTP LAENGVRQCY
HYWPDEGSNL YHIYEVNLVS EHIWCEDFLV RSFYLKNLQT NETRTVTQFH FLSWYDRGVP
SSSRSLLDFR RKVNKCYRGR SCPIIVHCSD GAGRSGTYVL IDMVLNKMAK GAKEIDIAAT
LEHLRDQRPG MVQTKEQFEF ALTAVAEEVN AILKALPQ*

mutated AA sequence

MGPPLPLLLL LLLLLPPRVL PAAPSSVPRG RQLPGRLDGV FGRCQKVPAM DFYRYEVSPV
ALQRLRVALQ KLSGTGFTWQ DDYTQYVMDQ ELADLPKTYL RRPEASSPAR PSKHSVGSER
RYSREGGAAL ANALRRHLPF LEALSQAPAS DVLARTHTAQ DRPPAEGDDR FSESILTYVA
HTSALTYPPG SRTQLREDLL PRTLGQLQPD ELSPKVDSGV DRHHLMAALS AYAAQRPPAP
PGEGSLEPQY LLRAPSRMPR PLLAPAAPQK WPSPLGDSED PSSTGDGARI HTLLKDLQRQ
PAEVRGLNGL ELDGMAELMA GLMQGVDHGV ARGSPGRAAL GESGEQADGP KATLRGDSFP
DDGVQDDDDR LYQEVHRLSA TLGGLLQDHG SRLLPGALPF ARPLDMERKK SEHPESSLSS
EEETAGVENV KSQTYSKDLL GQQPHSEPGA AAFGELQNQM PGPSKEEQSL PAGAQEALSD
GLQLEVQPSE EEARGYIVTD RDPLRPEEGR RLVEDVARLL QVPSSAFADV EVLGPAVTFK
VSANVQNVTT EDVEKATVDN KDKLEETSGL KILQTGVGSK SKLKFLPPQA EQEDSTKFIA
LTLVSLACIL GVLLASGLIY CLRHSSQHRL KEKLSGLGGD PGADATAAYQ ELCRQRMATR
PPDRPEGPHT SRISSVSSQF SDGPIPSPSA RSSASSWSEE PVQSNMDIST GHMILSYMED
HLKNKNRLEK EWEALCAYQA EPNSSFVAQR EENVPKNRSL AVLTYDHSRV LLKAENSHSH
SDYINASPIM DHDPRNPAYI ATQGPLPATV ADFWQMVWES GCVVIVMLTP LAENGVRQCY
HYWPDEGSNL YHIYEVNLVS EHIWCEDFLV RSFYLKNLQT NETRTVTQFH FLSWYDRGVP
SSSRSLLDFR RKVNKCYRGR SCPIIVHCSD GAGRSGTYVL IDMVLNKMAK GAKEIDIAAT
LEHLRDQRPG MVQTKEQFEF ALTAVAEEVN AILKALPQ*

speed

1.19 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