mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999971452 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM074066)
known disease mutation: rs8298 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:127826568C>TN/A show variant in all transcripts IGV

HGNC symbol

BIN1

Ensembl transcript ID

ENST00000357970

Genbank transcript ID

NM_139344

UniProt peptide

O00499

alteration type

single base exchange

alteration region

CDS

DNA changes

c.451G>A
cDNA.796G>A
g.38364G>A

AA changes

D151N Score: 23 explain score(s)

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

151

frameshift

known variant

Reference ID: rs121909274
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8298 (pathogenic for Myopathy, centronuclear, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074066)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074066)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074066)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.119	1
	4.989	1
(flanking)	-0.276	0.976

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 marginally increased	38362	wt: 0.8355 / mu: 0.9079 (marginal change - not scored)	wt: GGACTACGACAGTGC mu: GGACTACAACAGTGC	ACTA\|cgac
Donor gained	38364	0.85	mu: ACTACAACAGTGCCC	TACA\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

151

mutated

all conserved

151

Ptroglodytes

all identical

ENSPTRG00000012423

151

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000000531

123

Mmusculus

all identical

ENSMUSG00000024381

151

Ggallus

all identical

ENSGALG00000011541

151

Trubripes

all identical

ENSTRUG00000013580

152

Drerio

all identical

ENSDARG00000042114

152

Dmelanogaster

all identical

FBgn0027356

146

Celegans

all identical

F58G6.1

142

Xtropicalis

all identical

ENSXETG00000000473

122

protein features

start (aa)	end (aa)	feature	details
29	276	DOMAIN	BAR.	lost
133	161	HELIX		lost
193	267	COILED	Potential.	might get lost (downstream of altered splice site)
205	268	HELIX		might get lost (downstream of altered splice site)
296	296	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
298	298	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
303	303	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
307	307	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
323	323	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
331	331	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
378	421	REGION	Clathrin-binding.	might get lost (downstream of altered splice site)
474	474	CONFLICT	A -> P (in Ref. 2; AAB63263).	might get lost (downstream of altered splice site)
481	481	CONFLICT	A -> S (in Ref. 10; AAC24126/AAC23750/ AAC23751).	might get lost (downstream of altered splice site)
510	510	CONFLICT	S -> C (in Ref. 7; AAC23440/AAC23441).	might get lost (downstream of altered splice site)
520	592	DOMAIN	SH3.	might get lost (downstream of altered splice site)
523	527	STRAND		might get lost (downstream of altered splice site)
528	528	CONFLICT	Q -> H (in Ref. 7; AAC23440/AAC23441).	might get lost (downstream of altered splice site)
535	537	STRAND		might get lost (downstream of altered splice site)
546	549	STRAND		might get lost (downstream of altered splice site)
555	557	HELIX		might get lost (downstream of altered splice site)
562	567	STRAND		might get lost (downstream of altered splice site)
568	572	HELIX		might get lost (downstream of altered splice site)
573	579	HELIX		might get lost (downstream of altered splice site)
576	576	CONFLICT	E -> K (in Ref. 7; AAC23440/AAC23441).	might get lost (downstream of altered splice site)
582	585	STRAND		might get lost (downstream of altered splice site)
586	588	HELIX		might get lost (downstream of altered splice site)
589	591	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1653 / 1653

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

551 / 551

position of stopcodon in wt / mu cDNA

1998 / 1998

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

346 / 346

chromosome

strand

-1

last intron/exon boundary

1891

theoretical NMD boundary in CDS

1495

length of CDS

1653

coding sequence (CDS) position

451

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

796

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

38364

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

127826568

original gDNA sequence snippet

GGCGCAAGCTGGTGGACTACGACAGTGCCCGGCACCACTAC

altered gDNA sequence snippet

GGCGCAAGCTGGTGGACTACAACAGTGCCCGGCACCACTAC

original cDNA sequence snippet

GGCGCAAGCTGGTGGACTACGACAGTGCCCGGCACCACTAC

altered cDNA sequence snippet

GGCGCAAGCTGGTGGACTACAACAGTGCCCGGCACCACTAC

wildtype AA sequence

MAEMGSKGVT AGKIASNVQK KLTRAQEKVL QKLGKADETK DEQFEQCVQN FNKQLTEGTR
LQKDLRTYLA SVKAMHEASK KLNECLQEVY EPDWPGRDEA NKIAENNDLL WMDYHQKLVD
QALLTMDTYL GQFPDIKSRI AKRGRKLVDY DSARHHYESL QTAKKKDEAK IAKPVSLLEK
AAPQWCQGKL QAHLVAQTNL LRNQAEEELI KAQKVFEEMN VDLQEELPSL WNSRVGFYVN
TFQSIAGLEE NFHKEMSKLN QNLNDVLVGL EKQHGSNTFT VKAQPSDNAP AKGNKSPSPP
DGSPAATPEI RVNHEPEPAG GATPGATLPK SPSQFEAPGP FSEQASLLDL DFDPLPPVTS
PVKAPTPSGQ SIPWDLWEPT ESPAGSLPSG EPSAAEGTFA VSWPSQTAEP GPAQPAEASE
VAGGTQPAAG AQEPGETAAS EAASSSLPAV VVETFPATVN GTVEGGSGAG RLDLPPGFMF
KVQAQHDYTA TDTDELQLKA GDVVLVIPFQ NPEEQDEGWL MGVKESDWNQ HKELEKCRGV
FPENFTERVP *

mutated AA sequence

MAEMGSKGVT AGKIASNVQK KLTRAQEKVL QKLGKADETK DEQFEQCVQN FNKQLTEGTR
LQKDLRTYLA SVKAMHEASK KLNECLQEVY EPDWPGRDEA NKIAENNDLL WMDYHQKLVD
QALLTMDTYL GQFPDIKSRI AKRGRKLVDY NSARHHYESL QTAKKKDEAK IAKPVSLLEK
AAPQWCQGKL QAHLVAQTNL LRNQAEEELI KAQKVFEEMN VDLQEELPSL WNSRVGFYVN
TFQSIAGLEE NFHKEMSKLN QNLNDVLVGL EKQHGSNTFT VKAQPSDNAP AKGNKSPSPP
DGSPAATPEI RVNHEPEPAG GATPGATLPK SPSQFEAPGP FSEQASLLDL DFDPLPPVTS
PVKAPTPSGQ SIPWDLWEPT ESPAGSLPSG EPSAAEGTFA VSWPSQTAEP GPAQPAEASE
VAGGTQPAAG AQEPGETAAS EAASSSLPAV VVETFPATVN GTVEGGSGAG RLDLPPGFMF
KVQAQHDYTA TDTDELQLKA GDVVLVIPFQ NPEEQDEGWL MGVKESDWNQ HKELEKCRGV
FPENFTERVP *

speed

0.70 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