mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999016922848 (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)

chr8:17796382A>GN/A show variant in all transcripts IGV

HGNC symbol

PCM1

Ensembl transcript ID

ENST00000518537

Genbank transcript ID

N/A

UniProt peptide

Q15154

alteration type

single base exchange

alteration region

CDS

DNA changes

c.476A>G
cDNA.756A>G
g.16034A>G

AA changes

N159S Score: 46 explain score(s)

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

159

frameshift

known variant

Reference ID: rs412750

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1239	980	2219
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.649	0.726
	2.302	0.919
(flanking)	0.045	0.919

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	16028	0.73	mu: TGCATCTACAAGCCC	CATC\|taca

distance from splice site

134

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

159

mutated

all conserved

159

Ptroglodytes

all conserved

ENSPTRG00000020026

159

Mmulatta

all conserved

ENSMMUG00000015487

159

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000031592

159

Ggallus

not conserved

ENSGALG00000013602

159

Trubripes

all conserved

ENSTRUG00000015999

160

LLGP

Drerio

not conserved

ENSDARG00000062198

161

EPTAS

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012460

157

protein features

start (aa)	end (aa)	feature	details
159	159	MOD_RES	Phosphoserine.	lost
218	301	COILED	Potential.	might get lost (downstream of altered splice site)
294	294	CONFLICT	R -> RG (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
311	312	CONFLICT	EQ -> DE (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
356	356	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
372	372	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
399	399	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
400	424	COILED	Potential.	might get lost (downstream of altered splice site)
405	405	CONFLICT	E -> K (in Ref. 3; AAH27477).	might get lost (downstream of altered splice site)
408	408	CONFLICT	Q -> K (in Ref. 3; AAH27477/AAH65022).	might get lost (downstream of altered splice site)
431	431	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
447	448	CONFLICT	SV -> CL (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
487	543	COILED	Potential.	might get lost (downstream of altered splice site)
651	682	COILED	Potential.	might get lost (downstream of altered splice site)
726	769	COILED	Potential.	might get lost (downstream of altered splice site)
760	760	CONFLICT	Q -> H (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
824	858	COILED	Potential.	might get lost (downstream of altered splice site)
861	861	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
866	866	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
869	869	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
872	872	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
877	877	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
946	946	CONFLICT	G -> R (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
952	952	CONFLICT	R -> T (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
960	960	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
991	991	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1004	1004	CONFLICT	Missing (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1063	1089	COILED	Potential.	might get lost (downstream of altered splice site)
1086	1086	CONFLICT	Q -> R (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1168	1168	CONFLICT	Q -> R (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1169	1169	CONFLICT	N -> I (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1170	1170	CONFLICT	S -> L (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1185	1185	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1187	1187	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1188	1188	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1231	1231	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1257	1257	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1260	1260	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1262	1262	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1279	1799	REGION	Interaction with HAP1.	might get lost (downstream of altered splice site)
1290	1290	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1314	1315	SITE	Breakpoint for translocation to form PCM1-JAK2 fusion protein.	might get lost (downstream of altered splice site)
1342	1342	CONFLICT	V -> L (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1369	1370	SITE	Breakpoint for translocation to form PCM1-JAK2 fusion protein.	might get lost (downstream of altered splice site)
1373	1373	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1382	1382	CONFLICT	R -> Q (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1435	1435	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1437	1437	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1470	1471	SITE	Breakpoint for translocation to form PCM1-JAK2 fusion protein.	might get lost (downstream of altered splice site)
1515	1539	COILED	Potential.	might get lost (downstream of altered splice site)
1532	1532	CONFLICT	T -> A (in Ref. 4; BAC03656).	might get lost (downstream of altered splice site)
1609	1610	SITE	Breakpoint for translocation to form PCM1-RET fusion protein.	might get lost (downstream of altered splice site)
1656	1656	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1697	1697	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1730	1730	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1765	1765	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1768	1768	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1776	1776	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1849	1849	CONFLICT	S -> G (in Ref. 4; BAC03656).	might get lost (downstream of altered splice site)
1853	1864	CONFLICT	PLEREATSKNDQ -> HWNEKPLVKMTK (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1872	1872	CONFLICT	C -> S (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
1913	2024	REGION	Interaction with BBS4.	might get lost (downstream of altered splice site)
1947	1948	SITE	Breakpoint for translocation to form PCM1-JAK2 fusion protein.	might get lost (downstream of altered splice site)
1977	1977	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1988	1988	CONFLICT	E -> V (in Ref. 4; BAC03656).	might get lost (downstream of altered splice site)
1998	1998	CONFLICT	I -> M (in Ref. 1; AAA60120).	might get lost (downstream of altered splice site)
2023	2023	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1593 / 1593

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

531 / 531

position of stopcodon in wt / mu cDNA

1873 / 1873

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

281 / 281

chromosome

strand

last intron/exon boundary

1686

theoretical NMD boundary in CDS

1355

length of CDS

1593

coding sequence (CDS) position

476

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

756

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

16034

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

17796382

original gDNA sequence snippet

GAGCAAAGATGCATCTACAAACCCCCCAAACAGAGAAACGA

altered gDNA sequence snippet

GAGCAAAGATGCATCTACAAGCCCCCCAAACAGAGAAACGA

original cDNA sequence snippet

GAGCAAAGATGCATCTACAAACCCCCCAAACAGAGAAACGA

altered cDNA sequence snippet

GAGCAAAGATGCATCTACAAGCCCCCCAAACAGAGAAACGA

wildtype AA sequence

MATGGGPFED GMNDQDLPNW SNENVDDRLN NMDWGAQQKK ANRSSEKNKK KFGVESDKRV
TNDISPESSP GVGRRRTKTP HTFPHSRYMS QMSVPEQAEL EKLKQRINFS DLDQRSIGSD
SQGRATAANN KRQLSENRKP FNFLPMQINT NKSKDASTNP PNRETIGSAQ CKELFASALS
NDLLQNCQVS EEDGRGEPAM ESSQIVSRLV QIRDYITKAS SMREDLVEKN ERSANVERLT
HLIDHLKEQE KSYMKFLKKI LARENEEEDV RTIDSAVGSG SVAESTSLNI DVQSEASDTT
ARDPQQEPME EIENLKKQHD LLKRMLQQQE QLRALQGRQA ALLALQHKAE QAIAVMDDSV
VAETAGSLSG VSITSELNEE LNDLIQRFHN QLRDSQPPAV PDNRRQAESL SLTREVSQSR
KPSASERLPD EKVELFSKMR VLQEKKQKMD KLLGELHTLR DQHLNNSSSS PQRSVDQRST
SAPSASVGLA PVVNGESNSL TSSVPYPTAS LVSQNESENE GHLNPSEKLQ *

mutated AA sequence

MATGGGPFED GMNDQDLPNW SNENVDDRLN NMDWGAQQKK ANRSSEKNKK KFGVESDKRV
TNDISPESSP GVGRRRTKTP HTFPHSRYMS QMSVPEQAEL EKLKQRINFS DLDQRSIGSD
SQGRATAANN KRQLSENRKP FNFLPMQINT NKSKDASTSP PNRETIGSAQ CKELFASALS
NDLLQNCQVS EEDGRGEPAM ESSQIVSRLV QIRDYITKAS SMREDLVEKN ERSANVERLT
HLIDHLKEQE KSYMKFLKKI LARENEEEDV RTIDSAVGSG SVAESTSLNI DVQSEASDTT
ARDPQQEPME EIENLKKQHD LLKRMLQQQE QLRALQGRQA ALLALQHKAE QAIAVMDDSV
VAETAGSLSG VSITSELNEE LNDLIQRFHN QLRDSQPPAV PDNRRQAESL SLTREVSQSR
KPSASERLPD EKVELFSKMR VLQEKKQKMD KLLGELHTLR DQHLNNSSSS PQRSVDQRST
SAPSASVGLA PVVNGESNSL TSSVPYPTAS LVSQNESENE GHLNPSEKLQ *

speed

1.08 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