mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.011501605018857 (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 CM140548)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:97614661T>AN/A show variant in all transcripts IGV

HGNC symbol

SDC2

Ensembl transcript ID

ENST00000522911

Genbank transcript ID

N/A

UniProt peptide

P34741

alteration type

single base exchange

alteration region

CDS

DNA changes

c.124T>A
cDNA.187T>A
g.109083T>A

AA changes

S42T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs1042381

database	homozygous (A/A)	heterozygous	allele carriers
1000G	149	882	1031
ExAC	2436	17566	20002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.015	0.981
	0.91	0.983
(flanking)	3.675	0.98

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	109075	wt: 0.75 / mu: 0.92	wt: AGAGCTGACAACATC mu: AGAGCTGACAACAAC	AGCT\|gaca
Donor gained	109078	0.51	mu: GCTGACAACAACTCG	TGAC\|aaca

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 identical

ENSPTRG00000020443

Mmulatta

all identical

ENSMMUG00000000963

Fcatus

all identical

ENSFCAG00000014598

Mmusculus

all identical

ENSMUSG00000022261

Ggallus

all identical

ENSGALG00000015999

Trubripes

all identical

ENSTRUG00000004101

Drerio

not conserved

ENSDARG00000002731

Dmelanogaster

not conserved

FBgn0010415

209

Celegans

not conserved

F57C7.3

100

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
19	144	TOPO_DOM	Extracellular (Potential).	lost
41	41	CARBOHYD	O-linked (Xyl...) (heparan sulfate) (Potential).	might get lost (downstream of altered splice site)
55	55	CARBOHYD	O-linked (Xyl...) (heparan sulfate) (Potential).	might get lost (downstream of altered splice site)
57	57	CARBOHYD	O-linked (Xyl...) (heparan sulfate) (Potential).	might get lost (downstream of altered splice site)
101	101	CARBOHYD	O-linked (GalNAc...).	might get lost (downstream of altered splice site)
142	143	SITE	Cleavage of ectodomain (Potential).	might get lost (downstream of altered splice site)
145	169	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
150	150	CONFLICT	I -> T (in Ref. 2; BAB15150).	might get lost (downstream of altered splice site)
170	201	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

519 / 519

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

173 / 173

position of stopcodon in wt / mu cDNA

582 / 582

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

64 / 64

chromosome

strand

last intron/exon boundary

419

theoretical NMD boundary in CDS

305

length of CDS

519

coding sequence (CDS) position

124

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

187

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

109083

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

97614661

original gDNA sequence snippet

AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA

altered gDNA sequence snippet

AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA

original cDNA sequence snippet

AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA

altered cDNA sequence snippet

AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA

wildtype AA sequence

MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TSRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*

mutated AA sequence

MYLDNSSIEE ASGVYPIDDD DYASASGSGA DEDVESPELT TTRPLPKILL TSAAPKVETT
TLNIQNKIPA QTKSPEETDK EKVHLSDSER KMDPAEEDTN VYTEKHSDSL FKRTEVLAAV
IAGGVIGFLF AIFLILLLVY RMRKKDEGSY DLGERKPSSA AYQKAPTKEF YA*

speed

0.17 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