mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999815 (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 CM0910116)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:31379109G>AN/A show variant in all transcripts IGV

HGNC symbol

MICA

Ensembl transcript ID

ENST00000399172

Genbank transcript ID

N/A

UniProt peptide

Q29983

alteration type

single base exchange

alteration region

CDS

DNA changes

c.457G>A
cDNA.551G>A
g.11549G>A

AA changes

E153K Score: 56 explain score(s)

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

153

frameshift

known variant

Reference ID: rs1051794

database	homozygous (A/A)	heterozygous	allele carriers
1000G	347	1132	1479
ExAC	3917	14776	18693

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910116)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.142	0
	-0.314	0
(flanking)	-0.386	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	11545	wt: 0.32 / mu: 0.93	wt: CGATATCTAGAATCC mu: CGATATCTAAAATCC	ATAT\|ctag
Donor increased	11552	wt: 0.48 / mu: 0.59	wt: TAGAATCCGGCGTAG mu: TAAAATCCGGCGTAG	GAAT\|ccgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

153

mutated

all conserved

153

Ptroglodytes

all identical

ENSPTRG00000017957

196

Mmulatta

all conserved

ENSMMUG00000006609

196

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000030689

188

protein features

start (aa)	end (aa)	feature	details
24	307	TOPO_DOM	Extracellular (Potential).	lost
149	151	STRAND		might get lost (downstream of altered splice site)
156	170	HELIX		might get lost (downstream of altered splice site)
177	196	HELIX		might get lost (downstream of altered splice site)
187	187	DISULFID		might get lost (downstream of altered splice site)
207	296	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
208	213	STRAND		might get lost (downstream of altered splice site)
210	210	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
217	233	STRAND		might get lost (downstream of altered splice site)
220	220	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
225	225	DISULFID		might get lost (downstream of altered splice site)
236	241	STRAND		might get lost (downstream of altered splice site)
248	250	TURN		might get lost (downstream of altered splice site)
251	253	STRAND		might get lost (downstream of altered splice site)
260	262	STRAND		might get lost (downstream of altered splice site)
261	261	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
264	273	STRAND		might get lost (downstream of altered splice site)
277	279	HELIX		might get lost (downstream of altered splice site)
280	286	STRAND		might get lost (downstream of altered splice site)
282	282	DISULFID		might get lost (downstream of altered splice site)
289	294	STRAND		might get lost (downstream of altered splice site)
308	328	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
329	383	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

870 / 870

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

290 / 290

position of stopcodon in wt / mu cDNA

964 / 964

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

95 / 95

chromosome

strand

last intron/exon boundary

994

theoretical NMD boundary in CDS

849

length of CDS

870

coding sequence (CDS) position

457

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

551

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

11549

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

31379109

original gDNA sequence snippet

AGGAACTACGGCGATATCTAGAATCCGGCGTAGTCCTGAGG

altered gDNA sequence snippet

AGGAACTACGGCGATATCTAAAATCCGGCGTAGTCCTGAGG

original cDNA sequence snippet

AGGAACTACGGCGATATCTAGAATCCGGCGTAGTCCTGAGG

altered cDNA sequence snippet

AGGAACTACGGCGATATCTAAAATCCGGCGTAGTCCTGAGG

wildtype AA sequence

MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLESGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPR NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL*

mutated AA sequence

MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLKSGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPR NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL*

speed

1.10 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