MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000411486
Querying Taster for transcript #2: ENST00000432087
Querying Taster for transcript #3: ENST00000441687
MT speed 3.13 s - this script 4.240292 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HJURP	polymorphism_automatic	5.84698955918839e-12	simple_aae		affected		S241C	single base exchange	rs3732215		show file
HJURP	polymorphism_automatic	5.84698955918839e-12	simple_aae		affected		S295C	single base exchange	rs3732215		show file
HJURP	polymorphism_automatic	5.84698955918839e-12	simple_aae		affected		S210C	single base exchange	rs3732215		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999994153 (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)

chr2:234750542G>CN/A show variant in all transcripts IGV

HGNC symbol

HJURP

Ensembl transcript ID

ENST00000432087

Genbank transcript ID

N/A

UniProt peptide

Q8NCD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.722C>G
cDNA.788C>G
g.12671C>G

AA changes

S241C Score: 112 explain score(s)

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

241

frameshift

known variant

Reference ID: rs3732215

database	homozygous (C/C)	heterozygous	allele carriers
1000G	376	999	1375
ExAC	14264	4239	18503

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.134	0
	-0.172	0
(flanking)	-0.103	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	12671	wt: 0.38 / mu: 0.51	wt: GAACTCCAGGAGGAG mu: GAACTGCAGGAGGAG	ACTC\|cagg

distance from splice site

310

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

241

mutated

not conserved

241

Ptroglodytes

all identical

ENSPTRG00000013062

295

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000009698

153

Mmusculus

not conserved

ENSMUSG00000044783

278

LHK

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
412	412	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
448	448	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
473	473	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
486	486	MOD_RES	Phosphoserine; by PKB/AKT1.	might get lost (downstream of altered splice site)
486	486	MUTAGEN	S->A: Loss of phosphorylation by AKT1 and binding to YWHAG.	might get lost (downstream of altered splice site)
613	613	CONFLICT	S -> C (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)
642	642	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
733	733	CONFLICT	E -> G (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2085 / 2085

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

695 / 695

position of stopcodon in wt / mu cDNA

2151 / 2151

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

2076

theoretical NMD boundary in CDS

1959

length of CDS

2085

coding sequence (CDS) position

722

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

788

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

12671

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

234750542

original gDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered gDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

original cDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered cDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

wildtype AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ PAVPQSPLKN ELRRKYLTQV DILLQGAEYF ECAGNRAGRD
VRVTPLPSLA SPAVPAPGYC SRISRKSPGD PAKPASSPRE WDPLHPSSTD MALVPRNDSL
SLQETSSSSF LSSQPFEDDD ICNVTISDLY AGMLHSMSRL LSTKPSSIIS TKTFIMQNWN
SRRRHRYKSR MNKTYCKGAR RSQRSSKENF IPCSEPVKGT GALRDCKNVL DVSCRKTGLK
LEKAFLEVNR PQIHKLDPSW KERKVTPSKY SSLIYFDSSA TYNLDEENRF RTLKWLISPV
KIVSRPTIRQ GHGENRQREI EIRFDQLHRE YCLSPRNQPR RMCLPDSWAM NMYRGGPASP
GGLQGLETRR LSLPSSKAKA KSLSEAFENL GKRSLEAGRC LPKSDSSSSL PKTNPTHSAT
RPQQTSDLHV QGNSSGIFRK SVSPSKTLSV PDKEVPGHGR NRYDEIKEEF DKLHQKYCLK
SPGQMTVPLC IGVSTDKASM EVRYQTEGFL GKLNPDPHFQ GFQKLPSSPL GCRKSLLGST
AIEAPSSTCV ARAITRDGTR DHQFPAKRPR LSEPQGSGRQ GNSLGASDGV DNTVRPGDQG
SSSQPNSEER GENTSYRMEE KSDFMLEKLE TKSV*

mutated AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ PAVPQSPLKN ELRRKYLTQV DILLQGAEYF ECAGNRAGRD
VRVTPLPSLA SPAVPAPGYC SRISRKSPGD PAKPASSPRE WDPLHPSSTD MALVPRNDSL
SLQETSSSSF LSSQPFEDDD ICNVTISDLY AGMLHSMSRL LSTKPSSIIS TKTFIMQNWN
CRRRHRYKSR MNKTYCKGAR RSQRSSKENF IPCSEPVKGT GALRDCKNVL DVSCRKTGLK
LEKAFLEVNR PQIHKLDPSW KERKVTPSKY SSLIYFDSSA TYNLDEENRF RTLKWLISPV
KIVSRPTIRQ GHGENRQREI EIRFDQLHRE YCLSPRNQPR RMCLPDSWAM NMYRGGPASP
GGLQGLETRR LSLPSSKAKA KSLSEAFENL GKRSLEAGRC LPKSDSSSSL PKTNPTHSAT
RPQQTSDLHV QGNSSGIFRK SVSPSKTLSV PDKEVPGHGR NRYDEIKEEF DKLHQKYCLK
SPGQMTVPLC IGVSTDKASM EVRYQTEGFL GKLNPDPHFQ GFQKLPSSPL GCRKSLLGST
AIEAPSSTCV ARAITRDGTR DHQFPAKRPR LSEPQGSGRQ GNSLGASDGV DNTVRPGDQG
SSSQPNSEER GENTSYRMEE KSDFMLEKLE TKSV*

speed

0.99 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
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999994153 (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)

chr2:234750542G>CN/A show variant in all transcripts IGV

HGNC symbol

HJURP

Ensembl transcript ID

ENST00000411486

Genbank transcript ID

NM_018410

UniProt peptide

Q8NCD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.884C>G
cDNA.950C>G
g.12671C>G

AA changes

S295C Score: 112 explain score(s)

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

295

frameshift

known variant

Reference ID: rs3732215

database	homozygous (C/C)	heterozygous	allele carriers
1000G	376	999	1375
ExAC	14264	4239	18503

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.134	0
	-0.172	0
(flanking)	-0.103	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	12671	wt: 0.38 / mu: 0.51	wt: GAACTCCAGGAGGAG mu: GAACTGCAGGAGGAG	ACTC\|cagg

distance from splice site

310

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

295

mutated

not conserved

295

Ptroglodytes

all identical

ENSPTRG00000013062

295

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000009698

153

Mmusculus

not conserved

ENSMUSG00000044783

278

LHK

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
412	412	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
448	448	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
473	473	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
486	486	MOD_RES	Phosphoserine; by PKB/AKT1.	might get lost (downstream of altered splice site)
486	486	MUTAGEN	S->A: Loss of phosphorylation by AKT1 and binding to YWHAG.	might get lost (downstream of altered splice site)
613	613	CONFLICT	S -> C (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)
642	642	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
733	733	CONFLICT	E -> G (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2247 / 2247

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

749 / 749

position of stopcodon in wt / mu cDNA

2313 / 2313

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

2238

theoretical NMD boundary in CDS

2121

length of CDS

2247

coding sequence (CDS) position

884

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

950

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

12671

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

234750542

original gDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered gDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

original cDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered cDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

wildtype AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ DSSMKPADRT DGSVQAAAWG PELPSHRTVL GADSKSGEVD
ATSDQEESVA WALAPAVPQS PLKNELRRKY LTQVDILLQG AEYFECAGNR AGRDVRVTPL
PSLASPAVPA PGYCSRISRK SPGDPAKPAS SPREWDPLHP SSTDMALVPR NDSLSLQETS
SSSFLSSQPF EDDDICNVTI SDLYAGMLHS MSRLLSTKPS SIISTKTFIM QNWNSRRRHR
YKSRMNKTYC KGARRSQRSS KENFIPCSEP VKGTGALRDC KNVLDVSCRK TGLKLEKAFL
EVNRPQIHKL DPSWKERKVT PSKYSSLIYF DSSATYNLDE ENRFRTLKWL ISPVKIVSRP
TIRQGHGENR QREIEIRFDQ LHREYCLSPR NQPRRMCLPD SWAMNMYRGG PASPGGLQGL
ETRRLSLPSS KAKAKSLSEA FENLGKRSLE AGRCLPKSDS SSSLPKTNPT HSATRPQQTS
DLHVQGNSSG IFRKSVSPSK TLSVPDKEVP GHGRNRYDEI KEEFDKLHQK YCLKSPGQMT
VPLCIGVSTD KASMEVRYQT EGFLGKLNPD PHFQGFQKLP SSPLGCRKSL LGSTAIEAPS
STCVARAITR DGTRDHQFPA KRPRLSEPQG SGRQGNSLGA SDGVDNTVRP GDQGSSSQPN
SEERGENTSY RMEEKSDFML EKLETKSV*

mutated AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ DSSMKPADRT DGSVQAAAWG PELPSHRTVL GADSKSGEVD
ATSDQEESVA WALAPAVPQS PLKNELRRKY LTQVDILLQG AEYFECAGNR AGRDVRVTPL
PSLASPAVPA PGYCSRISRK SPGDPAKPAS SPREWDPLHP SSTDMALVPR NDSLSLQETS
SSSFLSSQPF EDDDICNVTI SDLYAGMLHS MSRLLSTKPS SIISTKTFIM QNWNCRRRHR
YKSRMNKTYC KGARRSQRSS KENFIPCSEP VKGTGALRDC KNVLDVSCRK TGLKLEKAFL
EVNRPQIHKL DPSWKERKVT PSKYSSLIYF DSSATYNLDE ENRFRTLKWL ISPVKIVSRP
TIRQGHGENR QREIEIRFDQ LHREYCLSPR NQPRRMCLPD SWAMNMYRGG PASPGGLQGL
ETRRLSLPSS KAKAKSLSEA FENLGKRSLE AGRCLPKSDS SSSLPKTNPT HSATRPQQTS
DLHVQGNSSG IFRKSVSPSK TLSVPDKEVP GHGRNRYDEI KEEFDKLHQK YCLKSPGQMT
VPLCIGVSTD KASMEVRYQT EGFLGKLNPD PHFQGFQKLP SSPLGCRKSL LGSTAIEAPS
STCVARAITR DGTRDHQFPA KRPRLSEPQG SGRQGNSLGA SDGVDNTVRP GDQGSSSQPN
SEERGENTSY RMEEKSDFML EKLETKSV*

speed

1.09 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999994153 (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)

chr2:234750542G>CN/A show variant in all transcripts IGV

HGNC symbol

HJURP

Ensembl transcript ID

ENST00000441687

Genbank transcript ID

N/A

UniProt peptide

Q8NCD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.629C>G
cDNA.695C>G
g.12671C>G

AA changes

S210C Score: 112 explain score(s)

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

210

frameshift

known variant

Reference ID: rs3732215

database	homozygous (C/C)	heterozygous	allele carriers
1000G	376	999	1375
ExAC	14264	4239	18503

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.134	0
	-0.172	0
(flanking)	-0.103	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	12671	wt: 0.38 / mu: 0.51	wt: GAACTCCAGGAGGAG mu: GAACTGCAGGAGGAG	ACTC\|cagg

distance from splice site

310

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

210

mutated

not conserved

210

Ptroglodytes

all identical

ENSPTRG00000013062

295

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000009698

153

Mmusculus

not conserved

ENSMUSG00000044783

278

LHK

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
412	412	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
448	448	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
473	473	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
486	486	MOD_RES	Phosphoserine; by PKB/AKT1.	might get lost (downstream of altered splice site)
486	486	MUTAGEN	S->A: Loss of phosphorylation by AKT1 and binding to YWHAG.	might get lost (downstream of altered splice site)
613	613	CONFLICT	S -> C (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)
642	642	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
733	733	CONFLICT	E -> G (in Ref. 3; BAG63122).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1992 / 1992

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

664 / 664

position of stopcodon in wt / mu cDNA

2058 / 2058

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

1983

theoretical NMD boundary in CDS

1866

length of CDS

1992

coding sequence (CDS) position

629

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

695

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

12671

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

234750542

original gDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered gDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

original cDNA sequence snippet

CATCATGCAAAACTGGAACTCCAGGAGGAGGCACAGATATA

altered cDNA sequence snippet

CATCATGCAAAACTGGAACTGCAGGAGGAGGCACAGATATA

wildtype AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ CAGNRAGRDV RVTPLPSLAS PAVPAPGYCS RISRKSPGDP
AKPASSPREW DPLHPSSTDM ALVPRNDSLS LQETSSSSFL SSQPFEDDDI CNVTISDLYA
GMLHSMSRLL STKPSSIIST KTFIMQNWNS RRRHRYKSRM NKTYCKGARR SQRSSKENFI
PCSEPVKGTG ALRDCKNVLD VSCRKTGLKL EKAFLEVNRP QIHKLDPSWK ERKVTPSKYS
SLIYFDSSAT YNLDEENRFR TLKWLISPVK IVSRPTIRQG HGENRQREIE IRFDQLHREY
CLSPRNQPRR MCLPDSWAMN MYRGGPASPG GLQGLETRRL SLPSSKAKAK SLSEAFENLG
KRSLEAGRCL PKSDSSSSLP KTNPTHSATR PQQTSDLHVQ GNSSGIFRKS VSPSKTLSVP
DKEVPGHGRN RYDEIKEEFD KLHQKYCLKS PGQMTVPLCI GVSTDKASME VRYQTEGFLG
KLNPDPHFQG FQKLPSSPLG CRKSLLGSTA IEAPSSTCVA RAITRDGTRD HQFPAKRPRL
SEPQGSGRQG NSLGASDGVD NTVRPGDQGS SSQPNSEERG ENTSYRMEEK SDFMLEKLET
KSV*

mutated AA sequence

MLGTLRAMEG EDVEDDQLLQ KLRASRRRFQ RRMQRLIEKY NQPFEDTPVV QMATLTYETP
QGLRIWGGRL IKERNEGEIQ CAGNRAGRDV RVTPLPSLAS PAVPAPGYCS RISRKSPGDP
AKPASSPREW DPLHPSSTDM ALVPRNDSLS LQETSSSSFL SSQPFEDDDI CNVTISDLYA
GMLHSMSRLL STKPSSIIST KTFIMQNWNC RRRHRYKSRM NKTYCKGARR SQRSSKENFI
PCSEPVKGTG ALRDCKNVLD VSCRKTGLKL EKAFLEVNRP QIHKLDPSWK ERKVTPSKYS
SLIYFDSSAT YNLDEENRFR TLKWLISPVK IVSRPTIRQG HGENRQREIE IRFDQLHREY
CLSPRNQPRR MCLPDSWAMN MYRGGPASPG GLQGLETRRL SLPSSKAKAK SLSEAFENLG
KRSLEAGRCL PKSDSSSSLP KTNPTHSATR PQQTSDLHVQ GNSSGIFRKS VSPSKTLSVP
DKEVPGHGRN RYDEIKEEFD KLHQKYCLKS PGQMTVPLCI GVSTDKASME VRYQTEGFLG
KLNPDPHFQG FQKLPSSPLG CRKSLLGSTA IEAPSSTCVA RAITRDGTRD HQFPAKRPRL
SEPQGSGRQG NSLGASDGVD NTVRPGDQGS SSQPNSEERG ENTSYRMEEK SDFMLEKLET
KSV*

speed

1.05 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems