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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000298892
Querying Taster for transcript #2: ENST00000395805
Querying Taster for transcript #3: ENST00000417045
Querying Taster for transcript #4: ENST00000251071
Querying Taster for transcript #5: ENST00000308433
MT speed 0 s - this script 4.486226 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CAPRIN2	polymorphism_automatic	0	simple_aae		affected		M519V	single base exchange	rs2304630		show file
CAPRIN2	polymorphism_automatic	0	simple_aae		affected		M519V	single base exchange	rs2304630		show file
CAPRIN2	polymorphism_automatic	0	simple_aae		affected		M519V	single base exchange	rs2304630		show file
CAPRIN2	polymorphism_automatic	0	simple_aae		affected		M519V	single base exchange	rs2304630		show file
CAPRIN2	polymorphism_automatic	0	simple_aae		affected		M186V	single base exchange	rs2304630		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr12:30881809T>CN/A show variant in all transcripts IGV

HGNC symbol

CAPRIN2

Ensembl transcript ID

ENST00000298892

Genbank transcript ID

NM_023925

UniProt peptide

Q6IMN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1555A>G
cDNA.2306A>G
g.26077A>G

AA changes

M519V Score: 21 explain score(s)

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

519

frameshift

known variant

Reference ID: rs2304630

database	homozygous (C/C)	heterozygous	allele carriers
1000G	862	1057	1919
ExAC	20099	-7431	12668

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.134	0.073
	-0.563	0
(flanking)	-1.63	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	26076	wt: 0.28 / mu: 0.66	wt: CCAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACAC mu: CCAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACAC	ttcc\|ATGC
Donor gained	26076	0.90	mu: CCTTCCGTGCAGAGC	TTCC\|gtgc

distance from splice site

228

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

519

mutated

all conserved

519

Ptroglodytes

all conserved

ENSPTRG00000004802

519

Mmulatta

all conserved

ENSMMUG00000001359

518

Fcatus

all conserved

ENSFCAG00000007004

517

Mmusculus

all conserved

ENSMUSG00000030309

427

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0042134

525

LAEVLGTGRFHFLQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007516

410

protein features

start (aa)	end (aa)	feature	details
547	547	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
554	554	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
560	560	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
595	595	CONFLICT	V -> A (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
924	924	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
993	1127	DOMAIN	C1q.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3234 / 3234

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

1078 / 1078

position of stopcodon in wt / mu cDNA

3985 / 3985

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

752 / 752

chromosome

strand

-1

last intron/exon boundary

3417

theoretical NMD boundary in CDS

2615

length of CDS

3234

coding sequence (CDS) position

1555

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

2306

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

26077

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

30881809

original gDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered gDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

original cDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered cDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

wildtype AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSMQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEVFNV
NAPLPPRKEQ EIKESPYSPG YNQSFTTAST QTPPQCQLPS IHVEQTVHSQ ETANYHPDGT
IQVSNGSLAF YPAQTNVFPR PTQPFVNSRG SVRGCTRGGR LITNSYRSPG GYKGFDTYRG
LPSISNGNYS QLQFQAREYS GAPYSQRDNF QQCYKRGGTS GGPRANSRAG WSDSSQVSSP
ERDNETFNSG DSGQGDSRSM TPVDVPVTNP AATILPVHVY PLPQQMRVAF SAARTSNLAP
GTLDQPIVFD LLLNNLGETF DLQLGRFNCP VNGTYVFIFH MLKLAVNVPL YVNLMKNEEV
LVSAYANDGA PDHETASNHA ILQLFQGDQI WLRLHRGAIY GSSWKYSTFS GYLLYQD*

mutated AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSVQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEVFNV
NAPLPPRKEQ EIKESPYSPG YNQSFTTAST QTPPQCQLPS IHVEQTVHSQ ETANYHPDGT
IQVSNGSLAF YPAQTNVFPR PTQPFVNSRG SVRGCTRGGR LITNSYRSPG GYKGFDTYRG
LPSISNGNYS QLQFQAREYS GAPYSQRDNF QQCYKRGGTS GGPRANSRAG WSDSSQVSSP
ERDNETFNSG DSGQGDSRSM TPVDVPVTNP AATILPVHVY PLPQQMRVAF SAARTSNLAP
GTLDQPIVFD LLLNNLGETF DLQLGRFNCP VNGTYVFIFH MLKLAVNVPL YVNLMKNEEV
LVSAYANDGA PDHETASNHA ILQLFQGDQI WLRLHRGAIY GSSWKYSTFS GYLLYQD*

speed

0.62 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: 1 (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)

chr12:30881809T>CN/A show variant in all transcripts IGV

HGNC symbol

CAPRIN2

Ensembl transcript ID

ENST00000417045

Genbank transcript ID

NM_032156

UniProt peptide

Q6IMN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1555A>G
cDNA.2103A>G
g.26077A>G

AA changes

M519V Score: 21 explain score(s)

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

519

frameshift

known variant

Reference ID: rs2304630

database	homozygous (C/C)	heterozygous	allele carriers
1000G	862	1057	1919
ExAC	20099	-7431	12668

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.134	0.073
	-0.563	0
(flanking)	-1.63	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	26076	wt: 0.28 / mu: 0.66	wt: CCAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACAC mu: CCAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACAC	ttcc\|ATGC
Donor gained	26076	0.90	mu: CCTTCCGTGCAGAGC	TTCC\|gtgc

distance from splice site

228

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

519

mutated

all conserved

519

Ptroglodytes

all conserved

ENSPTRG00000004802

519

Mmulatta

all conserved

ENSMMUG00000001359

518

Fcatus

all conserved

ENSFCAG00000007004

517

Mmusculus

all conserved

ENSMUSG00000030309

427

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0042134

525

LAEVLGTGRFHFLQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007516

410

protein features

start (aa)	end (aa)	feature	details
547	547	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
554	554	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
560	560	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
595	595	CONFLICT	V -> A (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
924	924	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
993	1127	DOMAIN	C1q.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2883 / 2883

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

961 / 961

position of stopcodon in wt / mu cDNA

3431 / 3431

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

549 / 549

chromosome

strand

-1

last intron/exon boundary

3361

theoretical NMD boundary in CDS

2762

length of CDS

2883

coding sequence (CDS) position

1555

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

2103

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

26077

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

30881809

original gDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered gDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

original cDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered cDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

wildtype AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSMQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEAAIP
PGKQPSSLAS PNPPMAKGSE QGFQSPPASS SSVTINTAPF QAMQTVFNVN APLPPRKEQE
IKESPYSPGY NQSFTTASTQ TPPQCQLPSI HVEQTVHSQE TANYHPDGTI QVSNGSLAFY
PAQTNVFPRP TQPFVNSRGS VRGCTRGGRL ITNSYRSPGG YKGFDTYRGL PSISNGNYSQ
LQFQAREYSG APYSQRDNFQ QCYKRGGTSG GPRANSRANC FIMRNSLLLI KQQGGVILLR
*

mutated AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSVQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEAAIP
PGKQPSSLAS PNPPMAKGSE QGFQSPPASS SSVTINTAPF QAMQTVFNVN APLPPRKEQE
IKESPYSPGY NQSFTTASTQ TPPQCQLPSI HVEQTVHSQE TANYHPDGTI QVSNGSLAFY
PAQTNVFPRP TQPFVNSRGS VRGCTRGGRL ITNSYRSPGG YKGFDTYRGL PSISNGNYSQ
LQFQAREYSG APYSQRDNFQ QCYKRGGTSG GPRANSRANC FIMRNSLLLI KQQGGVILLR
*

speed

0.60 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr12:30881809T>CN/A show variant in all transcripts IGV

HGNC symbol

CAPRIN2

Ensembl transcript ID

ENST00000395805

Genbank transcript ID

NM_001206856

UniProt peptide

Q6IMN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1555A>G
cDNA.2103A>G
g.26077A>G

AA changes

M519V Score: 21 explain score(s)

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

519

frameshift

known variant

Reference ID: rs2304630

database	homozygous (C/C)	heterozygous	allele carriers
1000G	862	1057	1919
ExAC	20099	-7431	12668

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.134	0.073
	-0.563	0
(flanking)	-1.63	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	26076	wt: 0.28 / mu: 0.66	wt: CCAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACAC mu: CCAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACAC	ttcc\|ATGC
Donor gained	26076	0.90	mu: CCTTCCGTGCAGAGC	TTCC\|gtgc

distance from splice site

228

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

519

mutated

all conserved

519

Ptroglodytes

all conserved

ENSPTRG00000004802

519

Mmulatta

all conserved

ENSMMUG00000001359

518

Fcatus

all conserved

ENSFCAG00000007004

517

Mmusculus

all conserved

ENSMUSG00000030309

427

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0042134

525

LAEVLGTGRFHFLQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007516

410

protein features

start (aa)	end (aa)	feature	details
547	547	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
554	554	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
560	560	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
595	595	CONFLICT	V -> A (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
924	924	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
993	1127	DOMAIN	C1q.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2718 / 2718

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

906 / 906

position of stopcodon in wt / mu cDNA

3266 / 3266

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

549 / 549

chromosome

strand

-1

last intron/exon boundary

3196

theoretical NMD boundary in CDS

2597

length of CDS

2718

coding sequence (CDS) position

1555

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

2103

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

26077

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

30881809

original gDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered gDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

original cDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered cDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

wildtype AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSMQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QAAIPPGKQP SSLASPNPPM AKGSEQGFQS PPASSSSVTI
NTAPFQAMQT VFNVNAPLPP RKEQEIKESP YSPGYNQSFT TASTQTPPQC QLPSIHVEQT
VHSQETAQTN VFPRPTQPFV NSRGSVRGCT RGGRLITNSY RSPGGYKGFD TYRGLPSISN
GNYSQLQFQA REYSGAPYSQ RDNFQQCYKR GGTSGGPRAN SRANCFIMRN SLLLIKQQGG
VILLR*

mutated AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSVQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QAAIPPGKQP SSLASPNPPM AKGSEQGFQS PPASSSSVTI
NTAPFQAMQT VFNVNAPLPP RKEQEIKESP YSPGYNQSFT TASTQTPPQC QLPSIHVEQT
VHSQETAQTN VFPRPTQPFV NSRGSVRGCT RGGRLITNSY RSPGGYKGFD TYRGLPSISN
GNYSQLQFQA REYSGAPYSQ RDNFQQCYKR GGTSGGPRAN SRANCFIMRN SLLLIKQQGG
VILLR*

speed

0.80 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr12:30881809T>CN/A show variant in all transcripts IGV

HGNC symbol

CAPRIN2

Ensembl transcript ID

ENST00000251071

Genbank transcript ID

NM_001002259

UniProt peptide

Q6IMN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1555A>G
cDNA.2306A>G
g.26077A>G

AA changes

M519V Score: 21 explain score(s)

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

519

frameshift

known variant

Reference ID: rs2304630

database	homozygous (C/C)	heterozygous	allele carriers
1000G	862	1057	1919
ExAC	20099	-7431	12668

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.134	0.073
	-0.563	0
(flanking)	-1.63	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	26076	wt: 0.28 / mu: 0.66	wt: CCAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACAC mu: CCAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACAC	ttcc\|ATGC
Donor gained	26076	0.90	mu: CCTTCCGTGCAGAGC	TTCC\|gtgc

distance from splice site

228

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

519

mutated

all conserved

519

Ptroglodytes

all conserved

ENSPTRG00000004802

519

Mmulatta

all conserved

ENSMMUG00000001359

518

Fcatus

all conserved

ENSFCAG00000007004

517

Mmusculus

all conserved

ENSMUSG00000030309

427

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0042134

525

LAEVLGTGRFHFLQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000007516

410

protein features

start (aa)	end (aa)	feature	details
547	547	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
554	554	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
560	560	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
595	595	CONFLICT	V -> A (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
924	924	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
993	1127	DOMAIN	C1q.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3384 / 3384

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

1128 / 1128

position of stopcodon in wt / mu cDNA

4135 / 4135

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

752 / 752

chromosome

strand

-1

last intron/exon boundary

3567

theoretical NMD boundary in CDS

2765

length of CDS

3384

coding sequence (CDS) position

1555

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

2306

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

26077

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

30881809

original gDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered gDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

original cDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered cDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

wildtype AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSMQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEAAIP
PGKQPSSLAS PNPPMAKGSE QGFQSPPASS SSVTINTAPF QAMQTVFNVN APLPPRKEQE
IKESPYSPGY NQSFTTASTQ TPPQCQLPSI HVEQTVHSQE TAANYHPDGT IQVSNGSLAF
YPAQTNVFPR PTQPFVNSRG SVRGCTRGGR LITNSYRSPG GYKGFDTYRG LPSISNGNYS
QLQFQAREYS GAPYSQRDNF QQCYKRGGTS GGPRANSRAG WSDSSQVSSP ERDNETFNSG
DSGQGDSRSM TPVDVPVTNP AATILPVHVY PLPQQMRVAF SAARTSNLAP GTLDQPIVFD
LLLNNLGETF DLQLGRFNCP VNGTYVFIFH MLKLAVNVPL YVNLMKNEEV LVSAYANDGA
PDHETASNHA ILQLFQGDQI WLRLHRGAIY GSSWKYSTFS GYLLYQD*

mutated AA sequence

MEVQVSQASL GFELTSVEKS LREWSRLSRE VIAWLCPSSP NFILNFPPPP SASSVSMVQL
FSSPFGYQSP SGHSEEEREG NMKSAKPQVN HSQHGESQRA LSPLQSTLSS AASPSQAYET
YIENGLICLK HKIRNIEKKK LKLEDYKDRL KSGEHLNPDQ LEAVEKYEEV LHNLEFAKEL
QKTFSGLSLD LLKAQKKAQR REHMLKLEAE KKKLRTILQV QYVLQNLTQE HVQKDFKGGL
NGAVYLPSKE LDYLIKFSKL TCPERNESLS VEDQMEQSSL YFWDLLEGSE KAVVGTTYKH
LKDLLSKLLN SGYFESIPVP KNAKEKEVPL EEEMLIQSEK KTQLSKTESV KESESLMEFA
QPEIQPQEFL NRRYMTEVDY SNKQGEEQPW EADYARKPNL PKRWDMLTEP DGQEKKQESF
KSWEASGKHQ EVSKPAVSLE QRKQDTSKLR STLPEEQKKQ EISKSKPSPS QWKQDTPKSK
AGYVQEEQKK QETPKLWPVQ LQKEQDPKKQ TPKSWTPSVQ SEQNTTKSWT TPMCEEQDSK
QPETPKSWEN NVESQKHSLT SQSQISPKSW GVATASLIPN DQLLPRKLNT EPKDVPKPVH
QPVGSSSTLP KDPVLRKEKL QDLMTQIQGT CNFMQESVLD FDKPSSAIPT SQPPSATPGS
PVASKEQNLS SQSDFLQEPL QATSSPVTCS SNACLVTTDQ ASSGSETEFM TSETPEAAIP
PGKQPSSLAS PNPPMAKGSE QGFQSPPASS SSVTINTAPF QAMQTVFNVN APLPPRKEQE
IKESPYSPGY NQSFTTASTQ TPPQCQLPSI HVEQTVHSQE TAANYHPDGT IQVSNGSLAF
YPAQTNVFPR PTQPFVNSRG SVRGCTRGGR LITNSYRSPG GYKGFDTYRG LPSISNGNYS
QLQFQAREYS GAPYSQRDNF QQCYKRGGTS GGPRANSRAG WSDSSQVSSP ERDNETFNSG
DSGQGDSRSM TPVDVPVTNP AATILPVHVY PLPQQMRVAF SAARTSNLAP GTLDQPIVFD
LLLNNLGETF DLQLGRFNCP VNGTYVFIFH MLKLAVNVPL YVNLMKNEEV LVSAYANDGA
PDHETASNHA ILQLFQGDQI WLRLHRGAIY GSSWKYSTFS GYLLYQD*

speed

0.59 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr12:30881809T>CN/A show variant in all transcripts IGV

HGNC symbol

CAPRIN2

Ensembl transcript ID

ENST00000308433

Genbank transcript ID

N/A

UniProt peptide

Q6IMN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.556A>G
cDNA.2223A>G
g.26077A>G

AA changes

M186V Score: 21 explain score(s)

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

186

frameshift

known variant

Reference ID: rs2304630

database	homozygous (C/C)	heterozygous	allele carriers
1000G	862	1057	1919
ExAC	20099	-7431	12668

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.134	0.073
	-0.563	0
(flanking)	-1.63	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	26076	wt: 0.28 / mu: 0.66	wt: CCAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACAC mu: CCAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACAC	ttcc\|ATGC
Donor gained	26076	0.90	mu: CCTTCCGTGCAGAGC	TTCC\|gtgc

distance from splice site

228

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

186

mutated

all conserved

186

Ptroglodytes

all conserved

ENSPTRG00000004802

519

Mmulatta

all conserved

ENSMMUG00000001359

518

Fcatus

all conserved

ENSFCAG00000007004

517

Mmusculus

all conserved

ENSMUSG00000030309

427

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0042134

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000007516

359

protein features

start (aa)	end (aa)	feature	details
194	216	COILED	Potential.	might get lost (downstream of altered splice site)
298	298	CONFLICT	Y -> D (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
320	320	CONFLICT	P -> S (in Ref. 5; AAK83153).	might get lost (downstream of altered splice site)
547	547	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
554	554	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
560	560	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
595	595	CONFLICT	V -> A (in Ref. 4; BAB13830).	might get lost (downstream of altered splice site)
924	924	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
993	1127	DOMAIN	C1q.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2382 / 2382

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

794 / 794

position of stopcodon in wt / mu cDNA

4049 / 4049

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

1668 / 1668

chromosome

strand

-1

last intron/exon boundary

3481

theoretical NMD boundary in CDS

1763

length of CDS

2382

coding sequence (CDS) position

556

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

2223

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

26077

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

30881809

original gDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered gDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

original cDNA sequence snippet

CAAAGTCTTGGACACCTTCCATGCAGAGCGAACAGAACACC

altered cDNA sequence snippet

CAAAGTCTTGGACACCTTCCGTGCAGAGCGAACAGAACACC

wildtype AA sequence

MLIQSEKKTQ LSKTESVKES ESLMEFAQPE IQPQEFLNRR YMTEVDYSNK QGEEQPWEAD
YARKPNLPKR WDMLTEPDGQ EKKQESFKSW EASGKHQEVS KPAVSLEQRK QDTSKLRSTL
PEEQKKQEIS KSKPSPSQWK QDTPKSKAGY VQEEQKKQET PKLWPVQLQK EQDPKKQTPK
SWTPSMQSEQ NTTKSWTTPM CEEQDSKQPE TPKSWENNVE SQKHSLTSQS QISPKSWGVA
TASLIPNDQL LPRKLNTEPK DVPKPVHQPV GSSSTLPKDP VLRKEKLQDL MTQIQGTCNF
MQESVLDFDK PSSAIPTSQP PSATPGSPVA SKEQNLSSQS DFLQEPLQAT SSPVTCSSNA
CLVTTDQASS GSETEFMTSE TPEAAIPPGK QPSSLASPNP PMAKGSEQGF QSPPASSSSV
TINTAPFQAM QTVFNVNAPL PPRKEQEIKE SPYSPGYNQS FTTASTQTPP QCQLPSIHVE
QTVHSQETAN YHPDGTIQVS NGSLAFYPAQ TNVFPRPTQP FVNSRGSVRG CTRGGRLITN
SYRSPGGYKG FDTYRGLPSI SNGNYSQLQF QAREYSGAPY SQRDNFQQCY KRGGTSGGPR
ANSRAGWSDS SQVSSPERDN ETFNSGDSGQ GDSRSMTPVD VPVTNPAATI LPVHVYPLPQ
QMRVAFSAAR TSNLAPGTLD QPIVFDLLLN NLGETFDLQL GRFNCPVNGT YVFIFHMLKL
AVNVPLYVNL MKNEEVLVSA YANDGAPDHE TASNHAILQL FQGDQIWLRL HRGAIYGSSW
KYSTFSGYLL YQD*

mutated AA sequence

MLIQSEKKTQ LSKTESVKES ESLMEFAQPE IQPQEFLNRR YMTEVDYSNK QGEEQPWEAD
YARKPNLPKR WDMLTEPDGQ EKKQESFKSW EASGKHQEVS KPAVSLEQRK QDTSKLRSTL
PEEQKKQEIS KSKPSPSQWK QDTPKSKAGY VQEEQKKQET PKLWPVQLQK EQDPKKQTPK
SWTPSVQSEQ NTTKSWTTPM CEEQDSKQPE TPKSWENNVE SQKHSLTSQS QISPKSWGVA
TASLIPNDQL LPRKLNTEPK DVPKPVHQPV GSSSTLPKDP VLRKEKLQDL MTQIQGTCNF
MQESVLDFDK PSSAIPTSQP PSATPGSPVA SKEQNLSSQS DFLQEPLQAT SSPVTCSSNA
CLVTTDQASS GSETEFMTSE TPEAAIPPGK QPSSLASPNP PMAKGSEQGF QSPPASSSSV
TINTAPFQAM QTVFNVNAPL PPRKEQEIKE SPYSPGYNQS FTTASTQTPP QCQLPSIHVE
QTVHSQETAN YHPDGTIQVS NGSLAFYPAQ TNVFPRPTQP FVNSRGSVRG CTRGGRLITN
SYRSPGGYKG FDTYRGLPSI SNGNYSQLQF QAREYSGAPY SQRDNFQQCY KRGGTSGGPR
ANSRAGWSDS SQVSSPERDN ETFNSGDSGQ GDSRSMTPVD VPVTNPAATI LPVHVYPLPQ
QMRVAFSAAR TSNLAPGTLD QPIVFDLLLN NLGETFDLQL GRFNCPVNGT YVFIFHMLKL
AVNVPLYVNL MKNEEVLVSA YANDGAPDHE TASNHAILQL FQGDQIWLRL HRGAIYGSSW
KYSTFSGYLL YQD*

speed

0.59 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems