mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999476454299 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980578)
known disease mutation: rs6668 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:71909727C>TN/A show variant in all transcripts IGV

HGNC symbol

DYSF

Ensembl transcript ID

ENST00000409744

Genbank transcript ID

NM_001130977

UniProt peptide

O75923

alteration type

single base exchange

alteration region

CDS

DNA changes

c.6148C>T
cDNA.6289C>T
g.228876C>T

AA changes

R2050C Score: 180 explain score(s)

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

2050

frameshift

known variant

Reference ID: rs121908955

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

known disease mutation: rs6668 (pathogenic for Autosomal recessive limb-girdle muscular dystrophy type 2B|Qualitative or quantitative defects of dysferlin|Miyoshi muscular dystrophy 1|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980578)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980578)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980578)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.65	1
	1.079	1
(flanking)	5.429	1

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 increased	228883	wt: 0.2192 / mu: 0.2321 (marginal change - not scored)	wt: CATCCTGTGGCGGCGTTTCCGGTGGGCCATCATCCTCTTCA mu: CATCCTGTGGCGGTGTTTCCGGTGGGCCATCATCCTCTTCA	tccg\|GTGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2050

mutated

not conserved

2050

Ptroglodytes

all identical

ENSPTRG00000012049

2035

Mmulatta

all identical

ENSMMUG00000007176

2012

Fcatus

all identical

ENSFCAG00000004357

2012

Mmusculus

all identical

ENSMUSG00000033788

2062

Ggallus

all identical

ENSGALG00000016105

870

Trubripes

no homologue

Drerio

all identical

ENSDARG00000007370

1802

Dmelanogaster

no homologue

Celegans

no alignment

T05E8.1

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
2047	2067	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6267 / 6267

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

2089 / 2089

position of stopcodon in wt / mu cDNA

6408 / 6408

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

142 / 142

chromosome

strand

last intron/exon boundary

6370

theoretical NMD boundary in CDS

6178

length of CDS

6267

coding sequence (CDS) position

6148

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

6289

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

228876

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

71909727

original gDNA sequence snippet

TGAAGTTCATCCTGTGGCGGCGTTTCCGGTGGGCCATCATC

altered gDNA sequence snippet

TGAAGTTCATCCTGTGGCGGTGTTTCCGGTGGGCCATCATC

original cDNA sequence snippet

TGAAGTTCATCCTGTGGCGGCGTTTCCGGTGGGCCATCATC

altered cDNA sequence snippet

TGAAGTTCATCCTGTGGCGGTGTTTCCGGTGGGCCATCATC

wildtype AA sequence

MLCCLLVRAS NLPSAKKDRR SDPVASLTFR GVKKRTKVIK NSVNPVWNEG FEWDLKGIPL
DQGSELHVVV KDHETMGRNR FLGEAKVPLR EVLATPSLSA SFNAPLLDTK KQPTGASLVL
QVSYTPLPGA VPLFPPPTPL EPSPTLPDLD VVADTGGEED TEDQGLTGDE AEPFLDQSGG
PGAPTTPRKL PSRPPPHYPG IKRKRSAPTS RKLLSDKPQD FQIRVQVIEG RQLPGVNIKP
VVKVTAAGQT KRTRIHKGNS PLFNETLFFN LFDSPGELFD EPIFITVVDS RSLRTDALLG
EFRMDVGTIY REPRHAYLRK WLLLSDPDDF SAGARGYLKT SLCVLGPGDE APLERKDPSE
DKEDIESNLL RPTGVALRGA HFCLKVFRAE DLPQMDDAVM DNVKQIFGFE SNKKNLVDPF
VEVSFAGKML CSKILEKTAN PQWNQNITLP AMFPSMCEKM RIRIIDWDRL THNDIVATTY
LSMSKISAPG GEIEVDDYLG FLPTFGPCYI NLYGSPREFT GFPDPYTELN TGKGEGVAYR
GRLLLSLETK LVEHSEQKVE DLPADDILRV EKYLRRRKYS LFAAFYSATM LQDVDDAIQF
EVSIGNYGNK FDMTCLPLAS TTQYSRAVFD GCHYYYLPWG NVKPVVVLSS YWEDISHRIE
TQNQLLGIAD RLEAGLEQVH LALKAQCSTE DVDSLVAQLT DELIAGCSQP LGDIHETPSA
THLDQYLYQL RTHHLSQITE AALALKLGHS ELPAALEQAE DWLLRLRALA EEPQNSLPDI
VIWMLQGDKR VAYQRVPAHQ VLFSRRGANY CGKNCGKLQT IFLKYPMEKV PGARMPVQIR
VKLWFGLSVD EKEFNQFAEG KLSVFAETYE NETKLALVGN WGTTGLTYPK FSDVTGKIKL
PKDSFRPSAG WTWAGDWFVC PEKTLLHDMD AGHLSFVEEV FENQTRLPGG QWIYMSDNYT
DVNGEKVLPK DDIECPLGWK WEDEEWSTDL NRAVDEQGWE YSITIPPERK PKHWVPAEKM
YYTHRRRRWV RLRRRDLSQM EALKRHRQAE AEGEGWEYAS LFGWKFHLEY RKTDAFRRRR
WRRRMEPLEK TGPAAVFALE GALGGVMDDK SEDSMSVSTL SFGVNRPTIS CIFDYGNRYH
LRCYMYQARD LAAMDKDSFS DPYAIVSFLH QSQKTVVVKN TLNPTWDQTL IFYEIEIFGE
PATVAEQPPS IVVELYDHDT YGADEFMGRC ICQPSLERMP RLAWFPLTRG SQPSGELLAS
FELIQREKPA IHHIPGFEVQ ETSRILDESE DTDLPYPPPQ REANIYMVPQ NIKPALQRTA
IEILAWGLRN MKSYQLANIS SPSLVVECGG QTVQSCVIRN LRKNPNFDIC TLFMEVMLPR
EELYCPPITV KVIDNRQFGR RPVVGQCTIR SLESFLCDPY SAESPSPQGG PDDVSLLSPG
EDVLIDIDDK EPLIPIQLAD GLSSLAPTNT ASPPSSPHEE EFIDWWSKFF ASIGEREKCG
SYLEKDFDTL KVYDTQLENV EAFEGLSDFC NTFKLYRGKT QEETEDPSVI GEFKGLFKIY
PLPEDPAIPM PPRQFHQLAA QGPQECLVRI YIVRAFGLQP KDPNGKCDPY IKISIGKKSV
SDQDNYIPCT LEPVFGKMFE LTCTLPLEKD LKITLYDYDL LSKDEKIGET VVDLENRLLS
KFGARCGLPQ TYCVSGPNQW RDQLRPSQLL HLFCQQHRVK APVYRTDRVM FQDKEYSIEE
IEAGRIPNPH LGPVEERLAL HVLQQQGLVP EHVESRPLYS PLQPDIEQGK LQMWVDLFPK
ALGRPGPPFN ITPRRARRFF LRCIIWNTRD VILDDLSLTG EKMSDIYVKG WMIGFEEHKQ
KTDVHYRSLG GEGNFNWRFI FPFDYLPAEQ VCTIAKKDAF WRLDKTESKI PARVVFQIWD
NDKFSFDDFL GSLQLDLNRM PKPAKTAKKC SLDQLDDAFH PEWFVSLFEQ KTVKGWWPCV
AEEGEKKILA GKLEMTLEIV AESEHEERPA GQGRDEPNMN PKLEDPRRPD TSFLWFTSPY
KTMKFILWRR FRWAIILFII LFILLLFLAI FIYAFPNYAA MKLVKPFS*

mutated AA sequence

speed

0.65 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