mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999078187797 (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

ENST00000413539

Genbank transcript ID

NM_001130979

UniProt peptide

O75923

alteration type

single base exchange

alteration region

CDS

DNA changes

c.6217C>T
cDNA.6494C>T
g.228876C>T

AA changes

R2073C Score: 180 explain score(s)

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

2073

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

2073

mutated

not conserved

2073

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
2068	2080	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6336 / 6336

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

2112 / 2112

position of stopcodon in wt / mu cDNA

6613 / 6613

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

278 / 278

chromosome

strand

last intron/exon boundary

6575

theoretical NMD boundary in CDS

6247

length of CDS

6336

coding sequence (CDS) position

6217

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

6494

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

MLRVFILYAE NVHTPDTDIS DAYCSAVFAG VKKRTKVIKN SVNPVWNEGF EWDLKGIPLD
QGSELHVVVK DHETMGRNRF LGEAKVPLRE VLATPSLSAS FNAPLLDTKK QPTGASLVLQ
VSYTPLPGAV PLFPPPTPLE PSPTLPDLDV VAGGGQSRAE TWSLLSDSTM DTRYSGKKWP
APTDTGGEED 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 GEIEEEPAGA VKPSKASDLD
DYLGFLPTFG PCYINLYGSP REFTGFPDPY TELNTGKGEG VAYRGRLLLS LETKLVEHSE
QKVEDLPADD ILRVEKYLRR RKYSLFAAFY SATMLQDVDD AIQFEVSIGN YGNKFDMTCL
PLASTTQYSR AVFDGCHYYY LPWGNVKPVV VLSSYWEDIS HRIETQNQLL GIADRLEAGL
EQVHLALKAQ CSTEDVDSLV AQLTDELIAG CSQPLGDIHE TPSATHLDQY LYQLRTHHLS
QITEAALALK LGHSELPAAL EQAEDWLLRL RALAEEPQNS LPDIVIWMLQ GDKRVAYQRV
PAHQVLFSRR GANYCGKNCG KLQTIFLKYP MEKVPGARMP VQIRVKLWFG LSVDEKEFNQ
FAEGKLSVFA ETYENETKLA LVGNWGTTGL TYPKFSDVTG KIKLPKDSFR PSAGWTWAGD
WFVCPEKTLL HDMDAGHLSF VEEVFENQTR LPGGQWIYMS DNYTDVNGEK VLPKDDIECP
LGWKWEDEEW STDLNRAVDE QGWEYSITIP PERKPKHWVP AEKMYYTHRR RRWVRLRRRD
LSQMEALKRH RQAEAEGEGW EYASLFGWKF HLEYRKTDAF RRRRWRRRME PLEKTGPAAV
FALEGALGGV MDDKSEDSMS VSTLSFGVNR PTISCIFDYG NRYHLRCYMY QARDLAAMDK
DSFSDPYAIV SFLHQSQKTV VVKNTLNPTW DQTLIFYEIE IFGEPATVAE QPPSIVVELY
DHDTYGADEF MGRCICQPSL ERMPRLAWFP LTRGSQPSGE LLASFELIQR EKPAIHHIPG
FEVQETSRIL DESEDTDLPY PPPQREANIY MVPQNIKPAL QRTAIEILAW GLRNMKSYQL
ANISSPSLVV ECGGQTVQSC VIRNLRKNPN FDICTLFMEV MLPREELYCP PITVKVIDNR
QFGRRPVVGQ CTIRSLESFL CDPYSAESPS PQGGPDDVSL LSPGEDVLID IDDKEPLIPI
QEEEFIDWWS KFFASIGERE KCGSYLEKDF DTLKVYDTQL ENVEAFEGLS DFCNTFKLYR
GKTQEETEDP SVIGEFKGLF KIYPLPEDPA IPMPPRQFHQ LAAQGPQECL VRIYIVRAFG
LQPKDPNGKC DPYIKISIGK KSVSDQDNYI PCTLEPVFGK MFELTCTLPL EKDLKITLYD
YDLLSKDEKI GETVVDLENR LLSKFGARCG LPQTYCVSGP NQWRDQLRPS QLLHLFCQQH
RVKAPVYRTD RVMFQDKEYS IEEIEAGRIP NPHLGPVEER LALHVLQQQG LVPEHVESRP
LYSPLQPDIE QGKLQMWVDL FPKALGRPGP PFNITPRRAR RFFLRCIIWN TRDVILDDLS
LTGEKMSDIY VKGWMIGFEE HKQKTDVHYR SLGGEGNFNW RFIFPFDYLP AEQVCTIAKK
DAFWRLDKTE SKIPARVVFQ IWDNDKFSFD DFLGSLQLDL NRMPKPAKTA KKCSLDQLDD
AFHPEWFVSL FEQKTVKGWW PCVAEEGEKK ILAGKLEMTL EIVAESEHEE RPAGQGRDEP
NMNPKLEDPR RPDTSFLWFT SPYKTMKFIL WRRFRWAIIL FIILFILLLF LAIFIYAFPN
YAAMKLVKPF S*

mutated AA sequence

speed

1.23 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