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

0.64 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