mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999953 (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)

chr12:46321514A>TN/A show variant in all transcripts IGV

HGNC symbol

SCAF11

Ensembl transcript ID

ENST00000549162

Genbank transcript ID

N/A

UniProt peptide

Q99590

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1394T>A
cDNA.1512T>A
g.64390T>A

AA changes

F465Y Score: 22 explain score(s)

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

465

frameshift

known variant

Reference ID: rs7315731

database	homozygous (T/T)	heterozygous	allele carriers
1000G	444	1065	1509
ExAC	13157	6453	19610

regulatory features

H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.699	0
	0.495	0
(flanking)	-0.317	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 increased	64382	wt: 0.37 / mu: 0.79	wt: GGGAATGAAGATTTC mu: GGGAATGAAGATTAC	GAAT\|gaag

distance from splice site

1129

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

465

mutated

all conserved

465

Ptroglodytes

all identical

ENSPTRG00000004854

657

Mmulatta

all identical

ENSMMUG00000023791

658

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000033228

664

TEIIPACEHIQTENTEIIPVCG

Ggallus

no alignment

ENSGALG00000009672

n/a

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000045885

308

SQTLND

Dmelanogaster

no alignment

FBgn0037344

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
533	533	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
584	584	CONFLICT	I -> M (in Ref. 5; AAH40951).	might get lost (downstream of altered splice site)
608	608	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
614	614	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
623	623	CONFLICT	D -> G (in Ref. 5; AAH40951).	might get lost (downstream of altered splice site)
680	680	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
723	723	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
726	726	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
771	771	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
776	776	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
796	796	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
798	798	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
800	800	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
802	802	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
807	807	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
816	816	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
818	818	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
827	827	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
832	832	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
841	985	COMPBIAS	Arg-rich.	might get lost (downstream of altered splice site)
878	878	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
880	880	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
882	882	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
963	963	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1109	1109	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1127	1127	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1225	1285	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
1392	1392	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3816 / 3816

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

1272 / 1272

position of stopcodon in wt / mu cDNA

3934 / 3934

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

119 / 119

chromosome

strand

-1

last intron/exon boundary

3788

theoretical NMD boundary in CDS

3619

length of CDS

3816

coding sequence (CDS) position

1394

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

1512

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

64390

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

46321514

original gDNA sequence snippet

TACTTTTGGGAATGAAGATTTCAATAATATTCAAGACTCTG

altered gDNA sequence snippet

TACTTTTGGGAATGAAGATTACAATAATATTCAAGACTCTG

original cDNA sequence snippet

TACTTTTGGGAATGAAGATTTCAATAATATTCAAGACTCTG

altered cDNA sequence snippet

TACTTTTGGGAATGAAGATTACAATAATATTCAAGACTCTG

wildtype AA sequence

MFSSVSHSGE SSFTYRAYCT EFIEASEISA LIRQKRHELE LSWFPDTLPG IGRIGFIPWN
VETEVLPLIS SVLPRTIFPT STISFEHFGT SCKGYALAHT QEGEEKKQTS GTSNTRGSRR
KPAMTTPTRR STRNTRAETA SQSQRSPISD NSGCDAPGNS NPSLSVPSSA ESEKQTRQAP
KRKSVRRGRK PPLLKKKLRS SVAAPEKSSS NDSVDEETAE SDTSPVLEKE HQPDVDSSNI
CTVQTHVENQ SANCLKSCNE QIEESEKHTA NYDTEERVGS SSSESCAQDL PVLVGEEGEV
KKLENTGIEA NVLCLESEIS ENILEKGGDP LEKQDQISGL SQSEVKTDVC TVHLPNDFPT
CLTSESKVYQ PVSCPLSDLS ENVESVVNEE KITESSLVEI TEHKDFTLKT EELIESPKLE
SSEGEIIQTV DRQSVKSPEV QLLGHVETED VEIIATCDTF GNEDFNNIQD SENNLLKNNL
LNTKLEKSLE EKNESLTEHP RSTELPKTHI EQIQKHFSED NNEMIPMECD SFCSDQNESE
VEPSVNADLK QMNENSVTHC SENNMPSSDL ADEKVETVSQ PSESPKDTID KTKKPRTRRS
RFHSPSTTWS PNKDTPQEKK RPQSPSPRRE TGKESRKSQS PSPKNESARG RKKSRSQSPK
KDIARERRQS QSRSPKRDTT RESRRSESLS PRRETSRENK RSQPRVKDSS PGEKSRSQSR
ERESDRDGQR RERERRTRKW SRSRSHSRSP SRCRTKSKSS SFGRIDRDSY SPRWKGRWAN
DGWRCPRGND RYRKNDPEKQ NENTRKEKND IHLDADDPNS ADKHRNDCPN WITEKINSGP
DPRTRNPEKL KESHWEENRN ENSGNSWNKN FGSGWVSNRG RGRGNRGRGT YRSSFAYKDQ
NENRWQNRKP LSGNSNSSGS ESFKFVEQQS YKRKSEQEFS FDTPADRSGW TSASSWAVRK
TLPADVQNYY SRRGRNSSGP QSGWMKQEEE TSGQDSSLKD QTNQQVDGSQ LPINMMQPQM
NVMQQQMNAQ HQPMNIFPYP VGVHAPLMNI QRNPFNIHPQ LPLHLHTGVP LMQVATPTSV
SQGLPPPPPP PPPSQQVNYI ASQPDGKQLQ GIPSSSHVSN NMSTPVLPAP TAAPGNTGMV
QGPSSGNTSS SSHSKASNAA VKLAESKVSV AVEASADSSK TDKKLQIQEK AAQEVKLAIK
PFYQNKDITK EEYKEIVRKA VDKVCHSKSG EVNSTKVANL VKAYVDKYKY SRKGSQKKTL
EEPVSTEKNI G*

mutated AA sequence

MFSSVSHSGE SSFTYRAYCT EFIEASEISA LIRQKRHELE LSWFPDTLPG IGRIGFIPWN
VETEVLPLIS SVLPRTIFPT STISFEHFGT SCKGYALAHT QEGEEKKQTS GTSNTRGSRR
KPAMTTPTRR STRNTRAETA SQSQRSPISD NSGCDAPGNS NPSLSVPSSA ESEKQTRQAP
KRKSVRRGRK PPLLKKKLRS SVAAPEKSSS NDSVDEETAE SDTSPVLEKE HQPDVDSSNI
CTVQTHVENQ SANCLKSCNE QIEESEKHTA NYDTEERVGS SSSESCAQDL PVLVGEEGEV
KKLENTGIEA NVLCLESEIS ENILEKGGDP LEKQDQISGL SQSEVKTDVC TVHLPNDFPT
CLTSESKVYQ PVSCPLSDLS ENVESVVNEE KITESSLVEI TEHKDFTLKT EELIESPKLE
SSEGEIIQTV DRQSVKSPEV QLLGHVETED VEIIATCDTF GNEDYNNIQD SENNLLKNNL
LNTKLEKSLE EKNESLTEHP RSTELPKTHI EQIQKHFSED NNEMIPMECD SFCSDQNESE
VEPSVNADLK QMNENSVTHC SENNMPSSDL ADEKVETVSQ PSESPKDTID KTKKPRTRRS
RFHSPSTTWS PNKDTPQEKK RPQSPSPRRE TGKESRKSQS PSPKNESARG RKKSRSQSPK
KDIARERRQS QSRSPKRDTT RESRRSESLS PRRETSRENK RSQPRVKDSS PGEKSRSQSR
ERESDRDGQR RERERRTRKW SRSRSHSRSP SRCRTKSKSS SFGRIDRDSY SPRWKGRWAN
DGWRCPRGND RYRKNDPEKQ NENTRKEKND IHLDADDPNS ADKHRNDCPN WITEKINSGP
DPRTRNPEKL KESHWEENRN ENSGNSWNKN FGSGWVSNRG RGRGNRGRGT YRSSFAYKDQ
NENRWQNRKP LSGNSNSSGS ESFKFVEQQS YKRKSEQEFS FDTPADRSGW TSASSWAVRK
TLPADVQNYY SRRGRNSSGP QSGWMKQEEE TSGQDSSLKD QTNQQVDGSQ LPINMMQPQM
NVMQQQMNAQ HQPMNIFPYP VGVHAPLMNI QRNPFNIHPQ LPLHLHTGVP LMQVATPTSV
SQGLPPPPPP PPPSQQVNYI ASQPDGKQLQ GIPSSSHVSN NMSTPVLPAP TAAPGNTGMV
QGPSSGNTSS SSHSKASNAA VKLAESKVSV AVEASADSSK TDKKLQIQEK AAQEVKLAIK
PFYQNKDITK EEYKEIVRKA VDKVCHSKSG EVNSTKVANL VKAYVDKYKY SRKGSQKKTL
EEPVSTEKNI G*

speed

0.76 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