mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.998087529657063 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:140262426C>TN/A show variant in all transcripts IGV

HGNC symbol

EXD3

Ensembl transcript ID

ENST00000342129

Genbank transcript ID

N/A

UniProt peptide

Q8N9H8

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.674G>A
g.55289G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11533158

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1293	950	2243
ExAC	29158	-25549	3609

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.211	0.211
	-0.239	0.211
(flanking)	1.873	0.257

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -162) | splice site change before start ATG (at aa -161) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	55294	wt: 0.9405 / mu: 0.9766 (marginal change - not scored)	wt: GCGACGTTGAAGCTG mu: ACGACGTTGAAGCTG	GACG\|ttga
Donor increased	55281	wt: 0.55 / mu: 0.78	wt: AGCCACGCTGGGCGC mu: AGCCACGCTGGGCAC	CCAC\|gctg
Donor gained	55285	0.81	mu: ACGCTGGGCACGACG	GCTG\|ggca

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
105	105	CONFLICT	Q -> R (in Ref. 1; BAC10986 and 2; BAB70838/BAC04356).	might get lost (downstream of altered splice site)
160	160	CONFLICT	A -> T (in Ref. 2; BAC04356 and 4; AAH37355/AAI10880).	might get lost (downstream of altered splice site)
249	249	CONFLICT	G -> S (in Ref. 2; BAC04356).	might get lost (downstream of altered splice site)
322	322	CONFLICT	E -> D (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)
517	571	DOMAIN	3'-5' exonuclease.	might get lost (downstream of altered splice site)
519	519	CONFLICT	S -> T (in Ref. 1; BAC10986).	might get lost (downstream of altered splice site)
545	545	CONFLICT	C -> Y (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

1157 / 1157

chromosome

strand

-1

last intron/exon boundary

2388

theoretical NMD boundary in CDS

1181

length of CDS

1545

coding sequence (CDS) position

N/A

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

674

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

55289

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

140262426

original gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered gDNA sequence snippet

GCCAGGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

original cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG

altered cDNA sequence snippet

GAGAAGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG

wildtype AA sequence

MELLLPEERL PAAVAVELRR FRLQGRATEA DSRLEVKDMK DRYYQLPIPR ENVHLLASWE
DLTRHEGALL QCHQVVGVDV EWTPVFVAGG RPRPSLLQVA VEGHVFLLDV LALSQPPTGQ
GAQAFSRLVA QLLSDPSITK LGYGMVGDLQ KLGTSCPALA HVEKQILGGM DLLLVHRQMR
VASVPAPAVD RARELRGLSL LVQQVLGTAL DKTQQLSNWD RRPLCEEQVI YAAADAYCLL
EVHQALCREP ARFHLSEDLA GSRRPRHRER PGARKPPGLQ KASAPAAPRQ GLARSLRCLG
VDARMLGNGE DHRRAAEVAR QEGRIILTSG QPFHKLRAQV GAGRCLSVDC SLKAQQQAKA
VLKHFNVRVT HADIFSRCQA CNCDQYLKVS RDMMKQLMWL SSHQEGPRSS GPAPDAAPEG
CTYDRPCRWL QMADLRAETP DMLADGTRLQ LAGVPVGVLR TPGLRCFYCC TGCGKVFWDG
SHLGRVATHF RDMLESAPSP CEPSPAPSPA SSPF*

mutated AA sequence

N/A

speed

0.63 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