mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997518139 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM152573)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31682453C>TN/A show variant in all transcripts IGV

HGNC symbol

ITPRID1

Ensembl transcript ID

ENST00000451887

Genbank transcript ID

NM_001257968

UniProt peptide

Q6ZRS4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1547C>T
cDNA.1559C>T
g.128750C>T

AA changes

A516V Score: 64 explain score(s)

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

516

frameshift

known variant

Reference ID: rs4141001

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1352	946	2298
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM152573)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.531	0.048
	0.574	0.21
(flanking)	1.166	0.348

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	128740	wt: 0.44 / mu: 0.53	wt: GGGCGAGCATGTCTTTTTCAAGCCAAGAAGCGAATGCCTTG mu: GGGCGAGCATGTCTTTTTCAAGCCAAGAAGTGAATGCCTTG	tcaa\|GCCA
Donor marginally increased	128743	wt: 0.9612 / mu: 0.9724 (marginal change - not scored)	wt: CAAGCCAAGAAGCGA mu: CAAGCCAAGAAGTGA	AGCC\|aaga

distance from splice site

158

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

516

mutated

not conserved

516

Ptroglodytes

all identical

ENSPTRG00000019051

490

Mmulatta

not conserved

ENSMMUG00000022484

290

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000037973

495

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000086805

458

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
793	834	COMPBIAS	Cys-rich.	might get lost (downstream of altered splice site)
802	802	CONFLICT	P -> S (in Ref. 1; BAC87235).	might get lost (downstream of altered splice site)
896	937	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3189 / 3189

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

1063 / 1063

position of stopcodon in wt / mu cDNA

3201 / 3201

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

13 / 13

chromosome

strand

last intron/exon boundary

3080

theoretical NMD boundary in CDS

3017

length of CDS

3189

coding sequence (CDS) position

1547

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

1559

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

128750

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

31682453

original gDNA sequence snippet

GTCTTTTTCAAGCCAAGAAGCGAATGCCTTGGAACAAAGGG

altered gDNA sequence snippet

GTCTTTTTCAAGCCAAGAAGTGAATGCCTTGGAACAAAGGG

original cDNA sequence snippet

GTCTTTTTCAAGCCAAGAAGCGAATGCCTTGGAACAAAGGG

altered cDNA sequence snippet

GTCTTTTTCAAGCCAAGAAGTGAATGCCTTGGAACAAAGGG

wildtype AA sequence

MPTTASCKTI SLLKLLYSVS LQNYSPMMAQ KSQGSDNLQE GQEKSKREIL KCTKSAWAPL
DEWLPPDPEE ESQSLTIPML EDSKQESIQQ WLDSGFFVSA NENFQQVIDR TVSLYEQGMV
QMTVKDYMRS LHQFSETPIL SRGTSFNSCY STASVPQSIP EWLEFWEIDP VEILLDLGFG
ADEPDICMQI PARFLGCGSA ARGINIRVFL EAQKQRMDIE NPNLYGRFRQ LEILDHVTNA
FSSLLSDVSI LPNRAEEKAG GESVQRTSVS AAKEHRRRMG KLLRRASKQN IRRDCNPEVS
ESFKVKDEVF VPFTKPWDCG AELAATSINH KQNHLSLSVE HQSLQACDDL LPYPPHGLLS
KQWPCSSMPA KQAPPSCVSE GSVKGRTQKE NLFQTNKLKS LSHLAGKGPD SFEMEEVQSF
EEETGNPLDM TSGTVGARVD RANSCQSDSS GFLEEPLEPL PLQMPSLPNS QSPAENGGRK
PRDQSHSLVS SQDCQLESDG PDSKSRASMS FSSQEANALE QRASVSVMEE EFLLEAMEGP
PELYIPDMAC AKTTTRGECP RKDSHLWQLL PMPHAEYEVT RPTATSKYDH PLGFMVTHVT
EMQDSFVRPE GAGKVQSHHN ESQRSPGNDH TQDKFLHVDS EAPREEESSG FCPHTNHSLL
VPESSSQCIP KHSEITPYAT DLAQTSEKLI PHLHKLPGDP AQVKSRSGTL GQILPGTEAE
MENLPLNTGS SRSVMTQMSS SLVSAAQRAV ALGTGPRGTS LECTVCDPVT ATETRLGTKA
RQLNDASIQT SALSNKTLTH GPQPLTKSVS LDSGFSSICP MGTCHAIPAH CCICCHHHPH
CHGERQSPGP EPSVCRHCLC SLTGHQEAQF MTTLKALQDT TVRELCSCTV HEMEAMKTIC
QSFREYLEEI EQHLMGQQAL FSRDMSEEER EEAEQLQTLR EALRQQVAEL EFQLGDRAQQ
IREGILLQLE VLTAEPPEHY SNLHQYNWIE ESNGQTSCSK IHPGMAPRTV FPPDDGQEAP
CSGELLSAEL DPFFFSSKAN NSAKDEKIKS KDFLKTQDSG LL*

mutated AA sequence

MPTTASCKTI SLLKLLYSVS LQNYSPMMAQ KSQGSDNLQE GQEKSKREIL KCTKSAWAPL
DEWLPPDPEE ESQSLTIPML EDSKQESIQQ WLDSGFFVSA NENFQQVIDR TVSLYEQGMV
QMTVKDYMRS LHQFSETPIL SRGTSFNSCY STASVPQSIP EWLEFWEIDP VEILLDLGFG
ADEPDICMQI PARFLGCGSA ARGINIRVFL EAQKQRMDIE NPNLYGRFRQ LEILDHVTNA
FSSLLSDVSI LPNRAEEKAG GESVQRTSVS AAKEHRRRMG KLLRRASKQN IRRDCNPEVS
ESFKVKDEVF VPFTKPWDCG AELAATSINH KQNHLSLSVE HQSLQACDDL LPYPPHGLLS
KQWPCSSMPA KQAPPSCVSE GSVKGRTQKE NLFQTNKLKS LSHLAGKGPD SFEMEEVQSF
EEETGNPLDM TSGTVGARVD RANSCQSDSS GFLEEPLEPL PLQMPSLPNS QSPAENGGRK
PRDQSHSLVS SQDCQLESDG PDSKSRASMS FSSQEVNALE QRASVSVMEE EFLLEAMEGP
PELYIPDMAC AKTTTRGECP RKDSHLWQLL PMPHAEYEVT RPTATSKYDH PLGFMVTHVT
EMQDSFVRPE GAGKVQSHHN ESQRSPGNDH TQDKFLHVDS EAPREEESSG FCPHTNHSLL
VPESSSQCIP KHSEITPYAT DLAQTSEKLI PHLHKLPGDP AQVKSRSGTL GQILPGTEAE
MENLPLNTGS SRSVMTQMSS SLVSAAQRAV ALGTGPRGTS LECTVCDPVT ATETRLGTKA
RQLNDASIQT SALSNKTLTH GPQPLTKSVS LDSGFSSICP MGTCHAIPAH CCICCHHHPH
CHGERQSPGP EPSVCRHCLC SLTGHQEAQF MTTLKALQDT TVRELCSCTV HEMEAMKTIC
QSFREYLEEI EQHLMGQQAL FSRDMSEEER EEAEQLQTLR EALRQQVAEL EFQLGDRAQQ
IREGILLQLE VLTAEPPEHY SNLHQYNWIE ESNGQTSCSK IHPGMAPRTV FPPDDGQEAP
CSGELLSAEL DPFFFSSKAN NSAKDEKIKS KDFLKTQDSG LL*

speed

1.09 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