mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 2.0078895964065e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000554698

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.372G>C
cDNA.880G>C
g.2637G>C

AA changes

L124F Score: 22 explain score(s)

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

124

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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
Acc increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

124

mutated

not conserved

124

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

233

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

240

Drerio

all identical

ENSDARG00000068215

240

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

237

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

558 / 558

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

186 / 186

position of stopcodon in wt / mu cDNA

1066 / 1066

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

509 / 509

chromosome

strand

-1

last intron/exon boundary

657

theoretical NMD boundary in CDS

length of CDS

558

coding sequence (CDS) position

372

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

880

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MAYYQPSLTA EYDEDSPGGD FDFFSNLVTK WEAAARLPGD STRQVVVRSG VVLGRGGGAM
GHMLLPFRLG LGGPIGSGHQ FFPWIHIGDL AGILTHALEA NHVHGVLNGV APSSATNAEF
AQTLGAALGR RAFIPLPSAV VQAVFGRQRA IMLLEGQKVI PQRTLATGYQ YSFPELGAAL
KEIVA*

mutated AA sequence

MAYYQPSLTA EYDEDSPGGD FDFFSNLVTK WEAAARLPGD STRQVVVRSG VVLGRGGGAM
GHMLLPFRLG LGGPIGSGHQ FFPWIHIGDL AGILTHALEA NHVHGVLNGV APSSATNAEF
AQTFGAALGR RAFIPLPSAV VQAVFGRQRA IMLLEGQKVI PQRTLATGYQ YSFPELGAAL
KEIVA*

speed

0.68 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