mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.0920675532748007 (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 CM1111866)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:43310415G>AN/A show variant in all transcripts IGV

HGNC symbol

SLC14A1

Ensembl transcript ID

ENST00000436407

Genbank transcript ID

N/A

UniProt peptide

Q13336

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298G>A
cDNA.845G>A
g.6324G>A

AA changes

E100K Score: 56 explain score(s)

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

100

frameshift

known variant

Reference ID: rs2298720

database	homozygous (A/A)	heterozygous	allele carriers
1000G	171	837	1008
ExAC	1984	13927	15911

known disease mutation at this position, please check HGMD for details (HGMD ID CM1111866)

regulatory features

H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.222	0.985
	2.968	1
(flanking)	1.374	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 increased	6319	wt: 0.22 / mu: 0.99	wt: TGACATGAAAGAACT mu: TGACATGAAAAAACT	ACAT\|gaaa
Donor marginally increased	6329	wt: 0.9455 / mu: 0.9457 (marginal change - not scored)	wt: GAACTTGCCAACCAG mu: AAACTTGCCAACCAG	ACTT\|gcca
Donor marginally increased	6321	wt: 0.8148 / mu: 0.8253 (marginal change - not scored)	wt: ACATGAAAGAACTTG mu: ACATGAAAAAACTTG	ATGA\|aaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

all conserved

100

Ptroglodytes

all identical

ENSPTRG00000009988

100

Mmulatta

all identical

ENSMMUG00000011037

Fcatus

all identical

ENSFCAG00000000240

Mmusculus

all identical

ENSMUSG00000059336

100

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
78	98	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
116	136	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
143	163	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
173	193	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
211	211	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
231	231	CONFLICT	G -> GVG (in Ref. 1).	might get lost (downstream of altered splice site)
243	263	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
281	301	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
310	330	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	353	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1338 / 1338

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

446 / 446

position of stopcodon in wt / mu cDNA

1885 / 1885

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

548 / 548

chromosome

strand

last intron/exon boundary

1712

theoretical NMD boundary in CDS

1114

length of CDS

1338

coding sequence (CDS) position

298

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

845

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

6324

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

43310415

original gDNA sequence snippet

ATGTCACCGGTGACATGAAAGAACTTGCCAACCAGCTTAAA

altered gDNA sequence snippet

ATGTCACCGGTGACATGAAAAAACTTGCCAACCAGCTTAAA

original cDNA sequence snippet

ATGTCACCGGTGACATGAAAGAACTTGCCAACCAGCTTAAA

altered cDNA sequence snippet

ATGTCACCGGTGACATGAAAAAACTTGCCAACCAGCTTAAA

wildtype AA sequence

MNGRSLIGGA GDARHGPVWK DPFGTKAGDA ARRGIARLSL ALADGSQEQE PEEEIAMEDS
PTMVRVDSPT MVRGENQVSP CQGRRCFPKA LGYVTGDMKE LANQLKDKPV VLQFIDWILR
GISQVVFVNN PVSGILILVG LLVQNPWWAL TGWLGTVVST LMALLLSQDR SLIASGLYGY
NATLVGVLMA VFSDKGDYFW WLLLPVCAMS MTCPIFSSAL NSMLSKWDLP VFTLPFNMAL
SMYLSATGHY NPFFPAKLVI PITTAPNISW SDLSALELLK SIPVGVGQIY GCDNPWTGGI
FLGAILLSSP LMCLHAAIGS LLGIAAGLSL SAPFEDIYFG LWGFNSSLAC IAMGGMFMAL
TWQTHLLALG CALFTAYLGV GMANFMAEVG LPACTWPFCL ATLLFLIMTT KNSNIYKMPL
SKVTYPEENR IFYLQAKKRM VESPL*

mutated AA sequence

MNGRSLIGGA GDARHGPVWK DPFGTKAGDA ARRGIARLSL ALADGSQEQE PEEEIAMEDS
PTMVRVDSPT MVRGENQVSP CQGRRCFPKA LGYVTGDMKK LANQLKDKPV VLQFIDWILR
GISQVVFVNN PVSGILILVG LLVQNPWWAL TGWLGTVVST LMALLLSQDR SLIASGLYGY
NATLVGVLMA VFSDKGDYFW WLLLPVCAMS MTCPIFSSAL NSMLSKWDLP VFTLPFNMAL
SMYLSATGHY NPFFPAKLVI PITTAPNISW SDLSALELLK SIPVGVGQIY GCDNPWTGGI
FLGAILLSSP LMCLHAAIGS LLGIAAGLSL SAPFEDIYFG LWGFNSSLAC IAMGGMFMAL
TWQTHLLALG CALFTAYLGV GMANFMAEVG LPACTWPFCL ATLLFLIMTT KNSNIYKMPL
SKVTYPEENR IFYLQAKKRM VESPL*

speed

1.23 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