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

ENST00000409210

Genbank transcript ID

N/A

UniProt peptide

Q6ZRS4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1193C>T
cDNA.1377C>T
g.128750C>T

AA changes

A398V Score: 64 explain score(s)

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

398

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

398

mutated

not conserved

398

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

459

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

2859 / 2859

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

953 / 953

position of stopcodon in wt / mu cDNA

3043 / 3043

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

185 / 185

chromosome

strand

last intron/exon boundary

3054

theoretical NMD boundary in CDS

2819

length of CDS

2859

coding sequence (CDS) position

1193

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

1377

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

MVQMTVKDYM RSLHQFSETP ILSRGTSFNS CYSTASVPQS IPEWLEFWEI DPVEILLDLG
FGADEPDICM QIPARFLGCG SAARGINIRV FLEAQKQRMD IENPNLYGRF RQLEILDHVT
NAFSSLLSDV SILPNRAEEK AGGESVQRTS VSAAKEHRRR MGKLLRRASK QNIRRDCNPE
VSESFKVKDE VFVPFTKPWD CGAELAATSI NHKQNHLSLS VEHQSLQACD DLLPYPPHGL
LSKQWPCSSM PAKQAPPSCV SEGSVKGRTQ KENLFQTNKL KSLSHLAGKG PDSFEMEEVQ
SFEEETGNPL DMTSGTVGAR VDRANSCQSD SSGFLEEPLE PLPLQMPSLP NSQSPAENGG
RKPRDQSHSL VSSQDCQLES DGPDSKSRAS MSFSSQEANA LEQRASVSVM EEEFLLEAME
GPPELYIPDM ACAKTTTRGE CPRKDSHLWQ LLPMPHAEYE VTRPTATSKY DHPLGFMVTH
VTEMQDSFVR PEGAGKVQSH HNESQRSPGN DHTQDKFLHV DSEAPREEES SGFCPHTNHS
LLVPESSSQC IPKHSEITPY ATDLAQTSEK LIPHLHKLPG DPAQVKSRSG TLGQILPGTE
AEMENLPLNT GSSRSVMTQM SSSLVSAAQR AVALGTGPRG TSLECTVCDP VTATETRLGT
KARQLNDASI QTSALSNKTL THGPQPLTKS VSLDSGFSSI CPMGTCHAIP AHCCICCHHH
PHCHGERQSP GPEPSVCRHC LCSLTGHQEA QFMTTLKALQ DTTVRELCSC TVHEMEAMKT
ICQSFREYLE EIEQHLMGQQ ALFSRDMSEE EREEAEQLQT LREALRQQVA ELEFQLGDRA
QQIREGILLQ LEVLTAEPPE HYSNLHQYNW IEESNGQTSC SKIHPGMAPR TVFPPDDGQE
APCSGGTQLA AFTPPTLENS TRMSPSSSAW AKLGPTPLSN CPVGEKDADV FL*

mutated AA sequence

MVQMTVKDYM RSLHQFSETP ILSRGTSFNS CYSTASVPQS IPEWLEFWEI DPVEILLDLG
FGADEPDICM QIPARFLGCG SAARGINIRV FLEAQKQRMD IENPNLYGRF RQLEILDHVT
NAFSSLLSDV SILPNRAEEK AGGESVQRTS VSAAKEHRRR MGKLLRRASK QNIRRDCNPE
VSESFKVKDE VFVPFTKPWD CGAELAATSI NHKQNHLSLS VEHQSLQACD DLLPYPPHGL
LSKQWPCSSM PAKQAPPSCV SEGSVKGRTQ KENLFQTNKL KSLSHLAGKG PDSFEMEEVQ
SFEEETGNPL DMTSGTVGAR VDRANSCQSD SSGFLEEPLE PLPLQMPSLP NSQSPAENGG
RKPRDQSHSL VSSQDCQLES DGPDSKSRAS MSFSSQEVNA LEQRASVSVM EEEFLLEAME
GPPELYIPDM ACAKTTTRGE CPRKDSHLWQ LLPMPHAEYE VTRPTATSKY DHPLGFMVTH
VTEMQDSFVR PEGAGKVQSH HNESQRSPGN DHTQDKFLHV DSEAPREEES SGFCPHTNHS
LLVPESSSQC IPKHSEITPY ATDLAQTSEK LIPHLHKLPG DPAQVKSRSG TLGQILPGTE
AEMENLPLNT GSSRSVMTQM SSSLVSAAQR AVALGTGPRG TSLECTVCDP VTATETRLGT
KARQLNDASI QTSALSNKTL THGPQPLTKS VSLDSGFSSI CPMGTCHAIP AHCCICCHHH
PHCHGERQSP GPEPSVCRHC LCSLTGHQEA QFMTTLKALQ DTTVRELCSC TVHEMEAMKT
ICQSFREYLE EIEQHLMGQQ ALFSRDMSEE EREEAEQLQT LREALRQQVA ELEFQLGDRA
QQIREGILLQ LEVLTAEPPE HYSNLHQYNW IEESNGQTSC SKIHPGMAPR TVFPPDDGQE
APCSGGTQLA AFTPPTLENS TRMSPSSSAW AKLGPTPLSN CPVGEKDADV FL*

speed

1.33 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