mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999974658 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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)

chr3:124802888C>TN/A show variant in all transcripts IGV

HGNC symbol

SLC12A8

Ensembl transcript ID

ENST00000314584

Genbank transcript ID

N/A

UniProt peptide

A0AV02

alteration type

single base exchange

alteration region

CDS

DNA changes

c.974G>A
cDNA.1765G>A
g.195134G>A

AA changes

R325Q Score: 43 explain score(s)

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

325

frameshift

known variant

Reference ID: rs2981482

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	15946	875	16821

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.12	0.001
	0.128	0
(flanking)	0.544	0.001

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 marginally increased	195125	wt: 0.7882 / mu: 0.7976 (marginal change - not scored)	wt: TCTGTGTCTCTCTCACTGCAGGAGCTTGCGGTCCCCTCAGG mu: TCTGTGTCTCTCTCACTGCAGGAGCTTGCAGTCCCCTCAGG	gcag\|GAGC
Donor gained	195139	0.39	mu: AGTCCCCTCAGGAGC	TCCC\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

325

mutated

all conserved

325

Ptroglodytes

all identical

ENSPTRG00000015317

664

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035506

567

DFFL

Ggallus

all conserved

ENSGALG00000012045

590

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074384

n/a

Dmelanogaster

not conserved

FBgn0024365

663

Celegans

no alignment

F10E7.9

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
309	331	TRANSMEM	Helical; (Potential).	lost
360	377	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
383	403	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
433	433	CONFLICT	L -> P (in Ref. 6; CAG33644).	might get lost (downstream of altered splice site)
481	481	CONFLICT	E -> D (in Ref. 3; BAB15571).	might get lost (downstream of altered splice site)
512	512	CONFLICT	P -> L (in Ref. 4; CAH18426).	might get lost (downstream of altered splice site)
555	555	CONFLICT	L -> P (in Ref. 4; CAD97969).	might get lost (downstream of altered splice site)
593	616	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
622	643	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
698	698	CONFLICT	R -> H (in Ref. 2; AAO49174).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1128 / 1128

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

376 / 376

position of stopcodon in wt / mu cDNA

1919 / 1919

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

792 / 792

chromosome

strand

-1

last intron/exon boundary

1760

theoretical NMD boundary in CDS

918

length of CDS

1128

coding sequence (CDS) position

974

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

1765

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

195134

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

124802888

original gDNA sequence snippet

CTCTCACTGCAGGAGCTTGCGGTCCCCTCAGGAGCAGATCA

altered gDNA sequence snippet

CTCTCACTGCAGGAGCTTGCAGTCCCCTCAGGAGCAGATCA

original cDNA sequence snippet

CAGTGGAGAAGGTGACTTGCGGTCCCCTCAGGAGCAGATCA

altered cDNA sequence snippet

CAGTGGAGAAGGTGACTTGCAGTCCCCTCAGGAGCAGATCA

wildtype AA sequence

MAGFNMGGDL REPAASIPPG SLAAVGISWF LYIIFVFLLG AICTREALRY DFLIAEKVSL
MGFLFLLGLY ISSLASCMGG LYGAPRILQC IAQEKVIPAL ACLGQGKGPN KTPVAAICLT
SLVTMAFVFV GQVNVLAPIV TINFMLTYVA VDYSYFSLSM CSCSLTPVPE PVLREGAEGL
HCSEHLLLEK APSYGSEGPA QRVLEGTLLE FTKDMDQLLQ LTRKLESSQP RQGEGNRTPE
SQKRKSKKAT KQTLQDSFLL DLKSPPSFPV EISDRLPAAS WEGQESCWNK QTSKSEGTQP
EGTYGEQLVP ELCNQSESSG EGDLRSPQEQ IILAPSLAKV DMEMTQLTQE NADFATRDRY
HHSSLVNREQ LMPHY*

mutated AA sequence

MAGFNMGGDL REPAASIPPG SLAAVGISWF LYIIFVFLLG AICTREALRY DFLIAEKVSL
MGFLFLLGLY ISSLASCMGG LYGAPRILQC IAQEKVIPAL ACLGQGKGPN KTPVAAICLT
SLVTMAFVFV GQVNVLAPIV TINFMLTYVA VDYSYFSLSM CSCSLTPVPE PVLREGAEGL
HCSEHLLLEK APSYGSEGPA QRVLEGTLLE FTKDMDQLLQ LTRKLESSQP RQGEGNRTPE
SQKRKSKKAT KQTLQDSFLL DLKSPPSFPV EISDRLPAAS WEGQESCWNK QTSKSEGTQP
EGTYGEQLVP ELCNQSESSG EGDLQSPQEQ IILAPSLAKV DMEMTQLTQE NADFATRDRY
HHSSLVNREQ LMPHY*

speed

0.81 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