mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997099 (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)

chr1:53535478G>AN/A show variant in all transcripts IGV

HGNC symbol

PODN

Ensembl transcript ID

ENST00000371500

Genbank transcript ID

NM_001199080

UniProt peptide

Q7Z5L7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.38G>A
cDNA.379G>A
g.7625G>A

AA changes

R13H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs1288386

database	homozygous (A/A)	heterozygous	allele carriers
1000G	379	1032	1411
ExAC	5482	15607	21089

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.083	0
	0.393	0
(flanking)	-0.133	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
Acc marginally decreased	7619	wt: 0.9673 / mu: 0.9602 (marginal change - not scored)	wt: TGTGTCCACTGTACCTCACAGGTTCCGTCAGCCCTGGCGCC mu: TGTGTCCACTGTACCTCACAGGTTCCATCAGCCCTGGCGCC	acag\|GTTC
Acc increased	7628	wt: 0.65 / mu: 0.81	wt: TGTACCTCACAGGTTCCGTCAGCCCTGGCGCCCAGGCGCAT mu: TGTACCTCACAGGTTCCATCAGCCCTGGCGCCCAGGCGCAT	gtca\|GCCC
Donor lost	7619	0.24	wt: TCACAGGTTCCGTCA	ACAG\|gttc
Donor gained	7628	0.38	mu: CCATCAGCCCTGGCG	ATCA\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000000749

Mmulatta

all identical

ENSMMUG00000007604

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000028600

n/a

Ggallus

no alignment

ENSGALG00000021869

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000019025

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	19	SIGNAL	Potential.	lost
59	96	DOMAIN	LRRNT.	might get lost (downstream of altered splice site)
97	118	REPEAT	LRR 1.	might get lost (downstream of altered splice site)
121	141	REPEAT	LRR 2.	might get lost (downstream of altered splice site)
147	168	REPEAT	LRR 3.	might get lost (downstream of altered splice site)
169	189	REPEAT	LRR 4.	might get lost (downstream of altered splice site)
192	212	REPEAT	LRR 5.	might get lost (downstream of altered splice site)
214	214	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
218	238	REPEAT	LRR 6.	might get lost (downstream of altered splice site)
239	260	REPEAT	LRR 7.	might get lost (downstream of altered splice site)
263	283	REPEAT	LRR 8.	might get lost (downstream of altered splice site)
281	281	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
289	310	REPEAT	LRR 9.	might get lost (downstream of altered splice site)
299	299	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
311	331	REPEAT	LRR 10.	might get lost (downstream of altered splice site)
334	357	REPEAT	LRR 11.	might get lost (downstream of altered splice site)
360	380	REPEAT	LRR 12.	might get lost (downstream of altered splice site)
381	402	REPEAT	LRR 13.	might get lost (downstream of altered splice site)
405	426	REPEAT	LRR 14.	might get lost (downstream of altered splice site)
410	410	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
431	452	REPEAT	LRR 15.	might get lost (downstream of altered splice site)
476	489	REPEAT	LRR 16.	might get lost (downstream of altered splice site)
502	522	REPEAT	LRR 17.	might get lost (downstream of altered splice site)
523	544	REPEAT	LRR 18.	might get lost (downstream of altered splice site)
547	568	REPEAT	LRR 19.	might get lost (downstream of altered splice site)
573	595	REPEAT	LRR 20.	might get lost (downstream of altered splice site)
598	611	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1929 / 1929

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

643 / 643

position of stopcodon in wt / mu cDNA

2270 / 2270

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

342 / 342

chromosome

strand

last intron/exon boundary

2298

theoretical NMD boundary in CDS

1906

length of CDS

1929

coding sequence (CDS) position

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

379

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

7625

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

53535478

original gDNA sequence snippet

CACTGTACCTCACAGGTTCCGTCAGCCCTGGCGCCCAGGCG

altered gDNA sequence snippet

CACTGTACCTCACAGGTTCCATCAGCCCTGGCGCCCAGGCG

original cDNA sequence snippet

AGAACAGCCTGCCTGGTTCCGTCAGCCCTGGCGCCCAGGCG

altered cDNA sequence snippet

AGAACAGCCTGCCTGGTTCCATCAGCCCTGGCGCCCAGGCG

wildtype AA sequence

MEGEEAEQPA WFRQPWRPGA SDSAPPAGTM AQSRVLLLLL LLPPQLHLGP VLAVRAPGFG
RSGGHSLSPE ENEFAEEEPV LVLSPEEPGP GPAAVSCPRD CACSQEGVVD CGGIDLREFP
GDLPEHTNHL SLQNNQLEKI YPEELSRLHR LETLNLQNNR LTSRGLPEKA FEHLTNLNYL
YLANNKLTLA PRFLPNALIS VDFAANYLTK IYGLTFGQKP NLRSVYLHNN KLADAGLPDN
MFNGSSNVEV LILSSNFLRH VPKHLPPALY KLHLKNNKLE KIPPGAFSEL SSLRELYLQN
NYLTDEGLDN ETFWKLSSLE YLDLSSNNLS RVPAGLPRSL VLLHLEKNAI RSVDANVLTP
IRSLEYLLLH SNQLREQGIH PLAFQGLKRL HTVHLYNNAL ERVPSGLPRR VRTLMILHNQ
ITGIGREDFA TTYFLEELNL SYNRITSPQV HRDAFRKLRL LRSLDLSGNR LHTLPPGLPR
NVHVLKVKRN ELAALARGAL VGMAQLRELY LTSNRLRSRA LGPRAWVDLA HLQLLDIAGN
QLTEIPEGLP ESLEYLYLQN NKISAVPANA FDSTPNLKGI FLRFNKLAVG SVVDSAFRRL
KHLQVLDIEG NLEFGDISKD RGRLGKEKEE EEEEEEEEEE TR*

mutated AA sequence

MEGEEAEQPA WFHQPWRPGA SDSAPPAGTM AQSRVLLLLL LLPPQLHLGP VLAVRAPGFG
RSGGHSLSPE ENEFAEEEPV LVLSPEEPGP GPAAVSCPRD CACSQEGVVD CGGIDLREFP
GDLPEHTNHL SLQNNQLEKI YPEELSRLHR LETLNLQNNR LTSRGLPEKA FEHLTNLNYL
YLANNKLTLA PRFLPNALIS VDFAANYLTK IYGLTFGQKP NLRSVYLHNN KLADAGLPDN
MFNGSSNVEV LILSSNFLRH VPKHLPPALY KLHLKNNKLE KIPPGAFSEL SSLRELYLQN
NYLTDEGLDN ETFWKLSSLE YLDLSSNNLS RVPAGLPRSL VLLHLEKNAI RSVDANVLTP
IRSLEYLLLH SNQLREQGIH PLAFQGLKRL HTVHLYNNAL ERVPSGLPRR VRTLMILHNQ
ITGIGREDFA TTYFLEELNL SYNRITSPQV HRDAFRKLRL LRSLDLSGNR LHTLPPGLPR
NVHVLKVKRN ELAALARGAL VGMAQLRELY LTSNRLRSRA LGPRAWVDLA HLQLLDIAGN
QLTEIPEGLP ESLEYLYLQN NKISAVPANA FDSTPNLKGI FLRFNKLAVG SVVDSAFRRL
KHLQVLDIEG NLEFGDISKD RGRLGKEKEE EEEEEEEEEE TR*

speed

1.01 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