mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998712 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1311834)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:95561459A>GN/A show variant in all transcripts IGV

HGNC symbol

PDLIM5

Ensembl transcript ID

ENST00000437932

Genbank transcript ID

NM_001011513

UniProt peptide

Q96HC4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.814A>G
cDNA.965A>G
g.188423A>G

AA changes

T272A Score: 58 explain score(s)

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

272

frameshift

known variant

Reference ID: rs7690296

database	homozygous (G/G)	heterozygous	allele carriers
1000G	439	1063	1502
ExAC	12093	8581	20674

known disease mutation at this position, please check HGMD for details (HGMD ID CM1311834)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.1	0
	-2.699	0
(flanking)	0.511	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 increased	188430	wt: 0.40 / mu: 0.59	wt: CTCAAACAGCGCTACTTACTCAGGATCAGTGGCACCAGCCA mu: CTCAAACAGCGCTGCTTACTCAGGATCAGTGGCACCAGCCA	actc\|AGGA
Donor marginally increased	188414	wt: 0.6965 / mu: 0.7610 (marginal change - not scored)	wt: TCTCAAACAGCGCTA mu: TCTCAAACAGCGCTG	TCAA\|acag
Donor increased	188427	wt: 0.34 / mu: 0.38	wt: TACTTACTCAGGATC mu: TGCTTACTCAGGATC	CTTA\|ctca
Donor gained	188417	0.82	mu: CAAACAGCGCTGCTT	AACA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

272

mutated

not conserved

272

Ptroglodytes

all identical

ENSPTRG00000016292

381

Mmulatta

all identical

ENSMMUG00000022246

381

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000028273

381

Ggallus

not conserved

ENSGALG00000012211

382

Trubripes

all conserved

ENSTRUG00000005717

384

LIT

Drerio

not conserved

ENSDARG00000027600

425

Dmelanogaster

not conserved

FBgn0083919

1974

VFPPDLSDLNLN

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000019217

381

protein features

start (aa)	end (aa)	feature	details
309	309	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
313	313	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
335	335	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
409	411	STRAND		might get lost (downstream of altered splice site)
413	415	TURN		might get lost (downstream of altered splice site)
418	477	DOMAIN	LIM zinc-binding 1.	might get lost (downstream of altered splice site)
419	423	STRAND		might get lost (downstream of altered splice site)
431	434	STRAND		might get lost (downstream of altered splice site)
437	439	STRAND		might get lost (downstream of altered splice site)
441	443	TURN		might get lost (downstream of altered splice site)
447	449	STRAND		might get lost (downstream of altered splice site)
454	456	STRAND		might get lost (downstream of altered splice site)
458	463	STRAND		might get lost (downstream of altered splice site)
468	474	HELIX		might get lost (downstream of altered splice site)
477	536	DOMAIN	LIM zinc-binding 2.	might get lost (downstream of altered splice site)
536	596	DOMAIN	LIM zinc-binding 3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1464 / 1464

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

488 / 488

position of stopcodon in wt / mu cDNA

1615 / 1615

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

152 / 152

chromosome

strand

last intron/exon boundary

1526

theoretical NMD boundary in CDS

1324

length of CDS

1464

coding sequence (CDS) position

814

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

965

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

188423

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

95561459

original gDNA sequence snippet

GAAGAATCTCAAACAGCGCTACTTACTCAGGATCAGTGGCA

altered gDNA sequence snippet

GAAGAATCTCAAACAGCGCTGCTTACTCAGGATCAGTGGCA

original cDNA sequence snippet

GAAGAATCTCAAACAGCGCTACTTACTCAGGATCAGTGGCA

altered cDNA sequence snippet

GAAGAATCTCAAACAGCGCTGCTTACTCAGGATCAGTGGCA

wildtype AA sequence

MSNYSVSLVG PAPWGFRLQG GKDFNMPLTI SSLKDGGKAA QANVRIGDVV LSIDGINAQG
MTHLEAQNKI KGCTGSLNMT LQRASAAPKP EPVPVQKPTV TSVCSETSQE LAEGQRRGSQ
GDSKQQNGPP RKHIVERYTE FYHVPTHSDA SKKRLIEDTE DWRPRTGTTQ SRSFRILAQI
TGTEHLKESE ADNTKKANNS QEPSPQLASS VASTRSMPES LDSPTSGRPG VTSLTAAAAF
KPVGSTGVIK SPSWQRPNQG VPSTGRISNS ATYSGSVAPA NSALGQTQPS DQDTLVQRAE
HIPAGKRTPM CAHCNQVIRG PFLVALGKSW HPEEFNCAHC KNTMAYIGFV EEKGALYCEL
CYEKFFAPEC GRCQRKILGE VISALKQTWH VSCFVCVACG KPIRNNVFHL EDGEPYCETD
YYALFGTICH GCEFPIEAGD MFLEALGYTW HDTCFVCSVC CESLEGQTFF SKKDKPLCKK
HAHSVNF*

mutated AA sequence

MSNYSVSLVG PAPWGFRLQG GKDFNMPLTI SSLKDGGKAA QANVRIGDVV LSIDGINAQG
MTHLEAQNKI KGCTGSLNMT LQRASAAPKP EPVPVQKPTV TSVCSETSQE LAEGQRRGSQ
GDSKQQNGPP RKHIVERYTE FYHVPTHSDA SKKRLIEDTE DWRPRTGTTQ SRSFRILAQI
TGTEHLKESE ADNTKKANNS QEPSPQLASS VASTRSMPES LDSPTSGRPG VTSLTAAAAF
KPVGSTGVIK SPSWQRPNQG VPSTGRISNS AAYSGSVAPA NSALGQTQPS DQDTLVQRAE
HIPAGKRTPM CAHCNQVIRG PFLVALGKSW HPEEFNCAHC KNTMAYIGFV EEKGALYCEL
CYEKFFAPEC GRCQRKILGE VISALKQTWH VSCFVCVACG KPIRNNVFHL EDGEPYCETD
YYALFGTICH GCEFPIEAGD MFLEALGYTW HDTCFVCSVC CESLEGQTFF SKKDKPLCKK
HAHSVNF*

speed

0.62 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