mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999987 (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)

chr5:35692775T>AN/A show variant in all transcripts IGV

HGNC symbol

SPEF2

Ensembl transcript ID

ENST00000440995

Genbank transcript ID

N/A

UniProt peptide

Q9C093

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1848T>A
cDNA.1848T>A
g.74830T>A

AA changes

N616K Score: 94 explain score(s)

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

616

frameshift

known variant

Reference ID: rs7710284

database	homozygous (A/A)	heterozygous	allele carriers
1000G	406	976	1382
ExAC	3965	18838	22803

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.131	0.001
	-0.738	0
(flanking)	-0.578	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
Donor marginally increased	74834	wt: 0.8426 / mu: 0.8894 (marginal change - not scored)	wt: ATGATGAAGAAGATG mu: AAGATGAAGAAGATG	GATG\|aaga
Donor increased	74830	wt: 0.40 / mu: 0.85	wt: AAAAATGATGAAGAA mu: AAAAAAGATGAAGAA	AAAT\|gatg
Donor increased	74825	wt: 0.22 / mu: 0.86	wt: TTCAGAAAAATGATG mu: TTCAGAAAAAAGATG	CAGA\|aaaa
Donor marginally increased	74831	wt: 0.9677 / mu: 0.9867 (marginal change - not scored)	wt: AAAATGATGAAGAAG mu: AAAAAGATGAAGAAG	AATG\|atga
Donor gained	74824	0.32	mu: ATTCAGAAAAAAGAT	TCAG\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

616

mutated

not conserved

616

Ptroglodytes

not conserved

ENSPTRG00000016788

616

Mmulatta

not conserved

ENSMMUG00000018739

616

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000072663

559

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000042913

615

QTEH

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
732	758	COILED	Potential.	might get lost (downstream of altered splice site)
871	909	COILED	Potential.	might get lost (downstream of altered splice site)
982	982	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin).	might get lost (downstream of altered splice site)
1686	1712	COILED	Potential.	might get lost (downstream of altered splice site)
1698	1698	CONFLICT	D -> G (in Ref. 1; BAB15563).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5457 / 5457

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

1819 / 1819

position of stopcodon in wt / mu cDNA

5457 / 5457

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

1 / 1

chromosome

strand

last intron/exon boundary

5365

theoretical NMD boundary in CDS

5314

length of CDS

5457

coding sequence (CDS) position

1848

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

1848

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

74830

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

35692775

original gDNA sequence snippet

GTTCTACCAATTCAGAAAAATGATGAAGAAGATGCTCTACC

altered gDNA sequence snippet

GTTCTACCAATTCAGAAAAAAGATGAAGAAGATGCTCTACC

original cDNA sequence snippet

GTTCTACCAATTCAGAAAAATGATGAAGAAGATGCTCTACC

altered cDNA sequence snippet

GTTCTACCAATTCAGAAAAAAGATGAAGAAGATGCTCTACC

wildtype AA sequence

MSEILCQWLN KELKVSRTVS PKSFAKAFSS GYLLGEVLHK FELQDDFSEF LDSRVSSAKL
NNFSRLEPTL NLLGVQFDQN VAHGIITEKP GVATKLLYQL YIALQKKKKS GLTGVEMQTM
QRLTNLRLQN MKSDTFQERL RHMIPRQTDF NLMRITYRFQ EKYKHVKEDL AHLHFEKLER
FQKLKEEQRC FDIEKQYLNR RRQNEIMAKI QAAIIQIPKP ASNRTLKALE AQKMMKKKKE
AEDVADEIKK FEALIKKDLQ AKESASKTSL DTAGQTTTDL LNTYSDDEYI KKIQKRLEED
AFAREQREKR RRKLLMDQLI AHEAQEEAYR EEQLINRLMR QSQQERRIAV QLMHVRHEKE
VLWQNRIFRE KQHEERRLKD FQDALDREAA LAKQAKIDFE EQFLKEKRFH DQIAVERAQA
RYEKHYSVCA EILDQIVDLS TKVADYRMLT NNLIPYKLMH DWKELFFNAK PIYEQASVKT
LPANPSREQL TELEKRDLLD TNDYEEYKNM VGEWALPEEM VDNLPPSNNC ILGHILHRLA
EKSLPPRAES TTPELPSFAV KGCLLGKTLS GKTTILRSLQ KDFPIQILSI DTLVQEAIQA
FHDNEKVSEV LPIQKNDEED ALPVLQEEIK ESQDPQHVFS AGPVSDEVLP ETEGANADKT
PKAEEVKSSD SFLKLTTRAQ LGAKSEQLLK KGKSIPDVLL VDIIVNAINE IPVNQDCILD
GFPMTLNQAQ LLEEALTGCN RNLTEVERKK AQKSTLAIDP ATSKEIPLPS PAFDFVILLD
VSDTSSMSRM NDIIAEELSY KTAHEDISQR VAAENQDKDG DQNLRDQIQH RIIGFLDNWP
LLEQWFSEPE NILIKINAEI DKESLCEKVK EILTTEIAKK KNKVEKKLEE KEAEKKAAAS
LAELPLPTPP PAPPPEPEKE KEIHQSHVAS KTPTAKGKPQ SEAPHGKQES LQEGKGKKGE
TALKRKGSPK GKSSGGKVPV KKSPADSTDT SPVAIVPQPP KPGSEEWVYV NEPVPEEMPL
FLVPYWELIE NSYINTIKTV LRHLREDQHT VLAYLYEIRT SFQEFLKRPD HKQDFVAQWQ
ADFNSLPDDL WDDEETKAEL HQRVNDLRDR LWDICDARKE EAEQERLDII NESWLQDTLG
MTMNHFFSLM QAELNRFQDT KRLLQDYYWG MESKIPVEDN KRFTRIPLVQ LDSKDNSESQ
LRIPLVPRIS ISLETVTPKP KTKSVLKGKM DNSLENVESN FEADEKLVMD TWQQASLAVS
HMVAAEIHQR LMEEEKENQP ADPKEKSPQM GANKKVKKEP PKKKQEDKKP KGKSPPMAEA
TPVIVTTEEI AEIKRKNELR VKIKEEHLAA LQFEEIATQF RLELIKTKAL ALLEDLVTKV
VDVYKLMEKW LGERYLNEMA STEKLTDVAR YHIETSTKIQ NELYLSQEDF FINGNIKVFP
DPPPSIRPPP VEKEEDGTLT IEQLDSLRDQ FLDMAPKGII GNKAFTDILI DLVTLNLGTN
NFPSNWMHLT QPELQELTSL LTVNSEFVDW RKFLLVTSMP WPIPLEEELL ETLQKFKAVD
KEQLGTITFE QYMQAGLWFT GDEDIKIPEN PLEPLPFNRQ EHLIEFFFRL FADYEKDPPQ
LDYTQMLLYF ACHPDTVEGV YRALSVAVGT HVFQQVKASI PSAEKTSSTD AGPAEEFPEP
EENAAREERK LKDDTEKREQ KDEEIPENAN NEKMSMETLL KVFKGGSEAQ DSNRFASHLK
IENIYAEGFI KTFQDLGAKN LEPIEVAVLL KHPFIQDLIS NYSDYKFPVH IIYVVEMIVC
AKGWAPLPSG KQCARWRN*

mutated AA sequence

MSEILCQWLN KELKVSRTVS PKSFAKAFSS GYLLGEVLHK FELQDDFSEF LDSRVSSAKL
NNFSRLEPTL NLLGVQFDQN VAHGIITEKP GVATKLLYQL YIALQKKKKS GLTGVEMQTM
QRLTNLRLQN MKSDTFQERL RHMIPRQTDF NLMRITYRFQ EKYKHVKEDL AHLHFEKLER
FQKLKEEQRC FDIEKQYLNR RRQNEIMAKI QAAIIQIPKP ASNRTLKALE AQKMMKKKKE
AEDVADEIKK FEALIKKDLQ AKESASKTSL DTAGQTTTDL LNTYSDDEYI KKIQKRLEED
AFAREQREKR RRKLLMDQLI AHEAQEEAYR EEQLINRLMR QSQQERRIAV QLMHVRHEKE
VLWQNRIFRE KQHEERRLKD FQDALDREAA LAKQAKIDFE EQFLKEKRFH DQIAVERAQA
RYEKHYSVCA EILDQIVDLS TKVADYRMLT NNLIPYKLMH DWKELFFNAK PIYEQASVKT
LPANPSREQL TELEKRDLLD TNDYEEYKNM VGEWALPEEM VDNLPPSNNC ILGHILHRLA
EKSLPPRAES TTPELPSFAV KGCLLGKTLS GKTTILRSLQ KDFPIQILSI DTLVQEAIQA
FHDNEKVSEV LPIQKKDEED ALPVLQEEIK ESQDPQHVFS AGPVSDEVLP ETEGANADKT
PKAEEVKSSD SFLKLTTRAQ LGAKSEQLLK KGKSIPDVLL VDIIVNAINE IPVNQDCILD
GFPMTLNQAQ LLEEALTGCN RNLTEVERKK AQKSTLAIDP ATSKEIPLPS PAFDFVILLD
VSDTSSMSRM NDIIAEELSY KTAHEDISQR VAAENQDKDG DQNLRDQIQH RIIGFLDNWP
LLEQWFSEPE NILIKINAEI DKESLCEKVK EILTTEIAKK KNKVEKKLEE KEAEKKAAAS
LAELPLPTPP PAPPPEPEKE KEIHQSHVAS KTPTAKGKPQ SEAPHGKQES LQEGKGKKGE
TALKRKGSPK GKSSGGKVPV KKSPADSTDT SPVAIVPQPP KPGSEEWVYV NEPVPEEMPL
FLVPYWELIE NSYINTIKTV LRHLREDQHT VLAYLYEIRT SFQEFLKRPD HKQDFVAQWQ
ADFNSLPDDL WDDEETKAEL HQRVNDLRDR LWDICDARKE EAEQERLDII NESWLQDTLG
MTMNHFFSLM QAELNRFQDT KRLLQDYYWG MESKIPVEDN KRFTRIPLVQ LDSKDNSESQ
LRIPLVPRIS ISLETVTPKP KTKSVLKGKM DNSLENVESN FEADEKLVMD TWQQASLAVS
HMVAAEIHQR LMEEEKENQP ADPKEKSPQM GANKKVKKEP PKKKQEDKKP KGKSPPMAEA
TPVIVTTEEI AEIKRKNELR VKIKEEHLAA LQFEEIATQF RLELIKTKAL ALLEDLVTKV
VDVYKLMEKW LGERYLNEMA STEKLTDVAR YHIETSTKIQ NELYLSQEDF FINGNIKVFP
DPPPSIRPPP VEKEEDGTLT IEQLDSLRDQ FLDMAPKGII GNKAFTDILI DLVTLNLGTN
NFPSNWMHLT QPELQELTSL LTVNSEFVDW RKFLLVTSMP WPIPLEEELL ETLQKFKAVD
KEQLGTITFE QYMQAGLWFT GDEDIKIPEN PLEPLPFNRQ EHLIEFFFRL FADYEKDPPQ
LDYTQMLLYF ACHPDTVEGV YRALSVAVGT HVFQQVKASI PSAEKTSSTD AGPAEEFPEP
EENAAREERK LKDDTEKREQ KDEEIPENAN NEKMSMETLL KVFKGGSEAQ DSNRFASHLK
IENIYAEGFI KTFQDLGAKN LEPIEVAVLL KHPFIQDLIS NYSDYKFPVH IIYVVEMIVC
AKGWAPLPSG KQCARWRN*

speed

1.24 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