mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999899394036734 (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 CM094608)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:89450587G>TN/A show variant in all transcripts IGV

HGNC symbol

MFGE8

Ensembl transcript ID

ENST00000539437

Genbank transcript ID

N/A

UniProt peptide

Q08431

alteration type

single base exchange

alteration region

CDS

DNA changes

c.202C>A
cDNA.339C>A
g.6056C>A

AA changes

L68M Score: 15 explain score(s)

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

frameshift

known variant

Reference ID: rs1878326

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1056	1085	2141
ExAC	23799	-14831	8968

known disease mutation at this position, please check HGMD for details (HGMD ID CM094608)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.77	1
	0.987	1
(flanking)	1.489	1

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 marginally increased	6058	wt: 0.4449 / mu: 0.4452 (marginal change - not scored)	wt: GGCCTGGAGAATGGG mu: GGCATGGAGAATGGG	CCTG\|gaga
Donor increased	6057	wt: 0.30 / mu: 0.44	wt: GGGCCTGGAGAATGG mu: GGGCATGGAGAATGG	GCCT\|ggag
Donor gained	6052	0.87	mu: CCACTGGGCATGGAG	ACTG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000007426

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030605

135

NTAVPTPAPTPDLSNNLAS

Ggallus

all conserved

ENSGALG00000006702

134

MDGDYACKCPSPFFGKTCHA

Trubripes

all conserved

ENSTRUG00000016888

169

Drerio

all conserved

ENSDARG00000045803

136

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000017772

137

LGDDFSCKCASPYIGKVCNI

protein features

start (aa)	end (aa)	feature	details
24	67	DOMAIN	EGF-like.	might get lost (downstream of altered splice site)
70	70	DISULFID	By similarity.	might get lost (downstream of altered splice site)
70	225	DOMAIN	F5/8 type C 1.	might get lost (downstream of altered splice site)
212	212	DISULFID	By similarity.	might get lost (downstream of altered splice site)
216	216	DISULFID	By similarity.	might get lost (downstream of altered splice site)
225	225	DISULFID	By similarity.	might get lost (downstream of altered splice site)
228	228	CARBOHYD	N-linked (GlcNAc...); atypical.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	387	DOMAIN	F5/8 type C 2.	might get lost (downstream of altered splice site)
238	238	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
268	268	CONFLICT	R -> W (in Ref. 5; CAD97938).	might get lost (downstream of altered splice site)
325	325	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
329	329	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
350	350	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
352	352	CONFLICT	S -> T (in Ref. 5; CAD97938).	might get lost (downstream of altered splice site)
387	387	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1140 / 1140

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

380 / 380

position of stopcodon in wt / mu cDNA

1277 / 1277

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

138 / 138

chromosome

strand

-1

last intron/exon boundary

1140

theoretical NMD boundary in CDS

952

length of CDS

1140

coding sequence (CDS) position

202

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

339

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

6056

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

89450587

original gDNA sequence snippet

AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC

altered gDNA sequence snippet

AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC

original cDNA sequence snippet

AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC

altered cDNA sequence snippet

AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC

wildtype AA sequence

MWPFPEGGNT IPILHTDICS KNPCHNGGLC EEISQEVRGD VFPSYTCTCL KGYAGNHCET
KCVEPLGLEN GNIANSQIAA SSVRVTFLGL QHWVPELARL NRAGMVNAWT PSSNDDNPWI
QVNLLRRMWV TGVVTQGASR LASHEYLKAF KVAYSLNGHE FDFIHDVNKK HKEFVGNWNK
NAVHVNLFET PVEAQYVRLY PTSCHTACTL RFELLGCELN GCANPLGLKN NSIPDKQITA
SSSYKTWGLH LFSWNPSYAR LDKQGNFNAW VAGSYGNDQW LQVDLGSSKE VTGIITQGAR
NFGSVQFVAS YKVAYSNDSA NWTEYQDPRT GSSKIFPGNW DNHSHKKNLF ETPILARYVR
ILPVAWHNRI ALRLELLGC*

mutated AA sequence

MWPFPEGGNT IPILHTDICS KNPCHNGGLC EEISQEVRGD VFPSYTCTCL KGYAGNHCET
KCVEPLGMEN GNIANSQIAA SSVRVTFLGL QHWVPELARL NRAGMVNAWT PSSNDDNPWI
QVNLLRRMWV TGVVTQGASR LASHEYLKAF KVAYSLNGHE FDFIHDVNKK HKEFVGNWNK
NAVHVNLFET PVEAQYVRLY PTSCHTACTL RFELLGCELN GCANPLGLKN NSIPDKQITA
SSSYKTWGLH LFSWNPSYAR LDKQGNFNAW VAGSYGNDQW LQVDLGSSKE VTGIITQGAR
NFGSVQFVAS YKVAYSNDSA NWTEYQDPRT GSSKIFPGNW DNHSHKKNLF ETPILARYVR
ILPVAWHNRI ALRLELLGC*

speed

0.92 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