mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999993 (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)

chr1:232574921T>CN/A show variant in all transcripts IGV

HGNC symbol

SIPA1L2

Ensembl transcript ID

ENST00000262861

Genbank transcript ID

N/A

UniProt peptide

Q9P2F8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3964A>G
cDNA.4191A>G
g.122384A>G

AA changes

T1322A Score: 58 explain score(s)

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

1322

frameshift

known variant

Reference ID: rs2275307

database	homozygous (C/C)	heterozygous	allele carriers
1000G	348	1068	1416
ExAC	5230	22307	27537

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.02	0.097
	0.18	0.005
(flanking)	-0.956	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	122394	wt: 0.44 / mu: 0.51	wt: CTACGCGTCCACCATCTCCGCCGGCAGTGCTGCGGAAGGCA mu: CTACGCGTCCGCCATCTCCGCCGGCAGTGCTGCGGAAGGCA	ccgc\|CGGC
Acc increased	122392	wt: 0.42 / mu: 0.55	wt: GGCTACGCGTCCACCATCTCCGCCGGCAGTGCTGCGGAAGG mu: GGCTACGCGTCCGCCATCTCCGCCGGCAGTGCTGCGGAAGG	ctcc\|GCCG
Donor gained	122383	0.59	mu: GCGTCCGCCATCTCC	GTCC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1322

mutated

not conserved

1322

Ptroglodytes

not conserved

ENSPTRG00000002114

1322

Mmulatta

not conserved

ENSMMUG00000012068

395

Fcatus

no alignment

ENSFCAG00000007249

n/a

Mmusculus

not conserved

ENSMUSG00000001995

1323

Ggallus

not conserved

ENSGALG00000011025

1317

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000088396

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000033496

1273

protein features

start (aa)	end (aa)	feature	details
1321	1384	COMPBIAS	Ser-rich.	lost
1406	1406	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1461	1461	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1478	1478	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1488	1488	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1549	1549	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1552	1552	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1654	1712	COILED	Potential.	might get lost (downstream of altered splice site)
1702	1702	CONFLICT	T -> I (in Ref. 2; BAB14273).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5169 / 5169

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

1723 / 1723

position of stopcodon in wt / mu cDNA

5396 / 5396

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

228 / 228

chromosome

strand

-1

last intron/exon boundary

5250

theoretical NMD boundary in CDS

4972

length of CDS

5169

coding sequence (CDS) position

3964

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

4191

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

122384

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

232574921

original gDNA sequence snippet

CTGTGCATGGCTACGCGTCCACCATCTCCGCCGGCAGTGCT

altered gDNA sequence snippet

CTGTGCATGGCTACGCGTCCGCCATCTCCGCCGGCAGTGCT

original cDNA sequence snippet

CTGTGCATGGCTACGCGTCCACCATCTCCGCCGGCAGTGCT

altered cDNA sequence snippet

CTGTGCATGGCTACGCGTCCGCCATCTCCGCCGGCAGTGCT

wildtype AA sequence

MSDPRQSQEE KHKLGRASSK FKDPPRIMQS DDYFARKFKA INGNMGPTTS LNASNSNETG
GGGPANGTPA VPKMGVRARV SEWPPKKDCS KELTCKALWE SRSQTSYESI TSVLQNGQSD
QSEGQQDEQL DLDFVEAKYT IGDIFVHSPQ RGLHPIRQRS NSDVTISDID AEDVLDQNAV
NPNTGAALHR EYGSTSSIDR QGLSGENFFA MLRGYRVENY DHKAMVPFGF PEFFRCDPAI
SPSLHAAAQI SRGEFVRISG LDYVDSALLM GRDRDKPFKR RLKSESVETS LFRKLRTVKS
EHETFKFTSE LEESRLERGI RPWNCQRCFA HYDVQSILFN INEAMATRAN VGKRKNITTG
ASAASQTQMP TGQTGNCESP LGSKEDLNSK ENLDADEGDG KSNDLVLSCP YFRNETGGEG
DRRIALSRAN SSSFSSGESC SFESSLSSHC TNAGVSVLEV PRENQPIHRE KVKRYIIEHI
DLGAYYYRKF FYGKEHQNYF GIDENLGPVA VSIRREKVED AKEKEGSQFN YRVAFRTSEL
TTLRGAILED AIPSTARHGT ARGLPLKEVL EYVIPELSIQ CLRQASNSPK VSEQLLKLDE
QGLSFQHKIG ILYCKAGQST EEEMYNNETA GPAFEEFLDL LGQRVRLKGF SKYRAQLDNK
TDSTGTHSLY TTYKDYELMF HVSTLLPYMP NNRQQLLRKR HIGNDIVTIV FQEPGALPFT
PKSIRSHFQH VFVIVKVHNP CTENVCYSVG VSRSKDVPPF GPPIPKGVTF PKSAVFRDFL
LAKVINAENA AHKSEKFRAM ATRTRQEYLK DLAENFVTTA TVDTSVKFSF ITLGAKKKEK
VKPRKDAHLF SIGAIMWHVI ARDFGQSADI ECLLGISNEF IMLIEKDSKN VVFNCSCRDV
IGWTSGLVSI KVFYERGECV LLSSVDNCAE DIREIVQRLV IVTRGCETVE MTLRRNGLGQ
LGFHVNFEGI VADVEPFGFA WKAGLRQGSR LVEICKVAVA TLTHEQMIDL LRTSVTVKVV
IIQPHDDGSP RRGCSELCRI PMVEYKLDSE GTPCEYKTPF RRNTTWHRVP TPALQPLSRA
SPIPGTPDRL PCQQLLQQAQ AAIPRSTSFD RKLPDGTRSS PSNQSSSSDP GPGGSGPWRP
QVGYDGCQSP LLLEHQGSGP LECDGARERE DTMEASRHPE TKWHGPPSKV LGSYKERALQ
KDGSCKDSPN KLSHIGDKSC SSHSSSNTLS SNTSSNSDDK HFGSGDLMDP ELLGLTYIKG
ASTDSGIDTA PCMPATILGP VHLAGSRSLI HSRAEQWADA ADVSGPDDEP AKLYSVHGYA
STISAGSAAE GSMGDLSEIS SHSSGSHHSG SPSAHCSKSS GSLDSSKVYI VSHSSGQQVP
GSMSKPYHRQ GAVNKYVIGW KKSEGSPPPE EPEVTECPGM YSEMDVMSTA TQHQTVVGDA
VAETQHVLSK EDFLKLMLPD SPLVEEGRRK FSFYGNLSPR RSLYRTLSDE SICSNRRGSS
FGSSRSSVLD QALPNDILFS TTPPYHSTLP PRAHPAPSMG SLRNEFWFSD GSLSDKSKCA
DPGLMPLPDT ATGLDWTHLV DAARAFEGLD SDEELGLLCH HTSYLDQRVA SFCTLTDMQH
GQDLEGAQEL PLCVDPGSGK EFMDTTGERS PSPLTGKVNQ LELILRQLQT DLRKEKQDKA
VLQAEVQHLR QDNMRLQEES QTATAQLRKF TEWFFTTIDK KS*

mutated AA sequence

MSDPRQSQEE KHKLGRASSK FKDPPRIMQS DDYFARKFKA INGNMGPTTS LNASNSNETG
GGGPANGTPA VPKMGVRARV SEWPPKKDCS KELTCKALWE SRSQTSYESI TSVLQNGQSD
QSEGQQDEQL DLDFVEAKYT IGDIFVHSPQ RGLHPIRQRS NSDVTISDID AEDVLDQNAV
NPNTGAALHR EYGSTSSIDR QGLSGENFFA MLRGYRVENY DHKAMVPFGF PEFFRCDPAI
SPSLHAAAQI SRGEFVRISG LDYVDSALLM GRDRDKPFKR RLKSESVETS LFRKLRTVKS
EHETFKFTSE LEESRLERGI RPWNCQRCFA HYDVQSILFN INEAMATRAN VGKRKNITTG
ASAASQTQMP TGQTGNCESP LGSKEDLNSK ENLDADEGDG KSNDLVLSCP YFRNETGGEG
DRRIALSRAN SSSFSSGESC SFESSLSSHC TNAGVSVLEV PRENQPIHRE KVKRYIIEHI
DLGAYYYRKF FYGKEHQNYF GIDENLGPVA VSIRREKVED AKEKEGSQFN YRVAFRTSEL
TTLRGAILED AIPSTARHGT ARGLPLKEVL EYVIPELSIQ CLRQASNSPK VSEQLLKLDE
QGLSFQHKIG ILYCKAGQST EEEMYNNETA GPAFEEFLDL LGQRVRLKGF SKYRAQLDNK
TDSTGTHSLY TTYKDYELMF HVSTLLPYMP NNRQQLLRKR HIGNDIVTIV FQEPGALPFT
PKSIRSHFQH VFVIVKVHNP CTENVCYSVG VSRSKDVPPF GPPIPKGVTF PKSAVFRDFL
LAKVINAENA AHKSEKFRAM ATRTRQEYLK DLAENFVTTA TVDTSVKFSF ITLGAKKKEK
VKPRKDAHLF SIGAIMWHVI ARDFGQSADI ECLLGISNEF IMLIEKDSKN VVFNCSCRDV
IGWTSGLVSI KVFYERGECV LLSSVDNCAE DIREIVQRLV IVTRGCETVE MTLRRNGLGQ
LGFHVNFEGI VADVEPFGFA WKAGLRQGSR LVEICKVAVA TLTHEQMIDL LRTSVTVKVV
IIQPHDDGSP RRGCSELCRI PMVEYKLDSE GTPCEYKTPF RRNTTWHRVP TPALQPLSRA
SPIPGTPDRL PCQQLLQQAQ AAIPRSTSFD RKLPDGTRSS PSNQSSSSDP GPGGSGPWRP
QVGYDGCQSP LLLEHQGSGP LECDGARERE DTMEASRHPE TKWHGPPSKV LGSYKERALQ
KDGSCKDSPN KLSHIGDKSC SSHSSSNTLS SNTSSNSDDK HFGSGDLMDP ELLGLTYIKG
ASTDSGIDTA PCMPATILGP VHLAGSRSLI HSRAEQWADA ADVSGPDDEP AKLYSVHGYA
SAISAGSAAE GSMGDLSEIS SHSSGSHHSG SPSAHCSKSS GSLDSSKVYI VSHSSGQQVP
GSMSKPYHRQ GAVNKYVIGW KKSEGSPPPE EPEVTECPGM YSEMDVMSTA TQHQTVVGDA
VAETQHVLSK EDFLKLMLPD SPLVEEGRRK FSFYGNLSPR RSLYRTLSDE SICSNRRGSS
FGSSRSSVLD QALPNDILFS TTPPYHSTLP PRAHPAPSMG SLRNEFWFSD GSLSDKSKCA
DPGLMPLPDT ATGLDWTHLV DAARAFEGLD SDEELGLLCH HTSYLDQRVA SFCTLTDMQH
GQDLEGAQEL PLCVDPGSGK EFMDTTGERS PSPLTGKVNQ LELILRQLQT DLRKEKQDKA
VLQAEVQHLR QDNMRLQEES QTATAQLRKF TEWFFTTIDK KS*

speed

1.20 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