mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999991435 (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 CM057213)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:20038466T>GN/A show variant in all transcripts IGV

HGNC symbol

SLC18A1

Ensembl transcript ID

ENST00000437980

Genbank transcript ID

NM_001142325

UniProt peptide

P54219

alteration type

single base exchange

alteration region

CDS

DNA changes

c.10A>C
cDNA.481A>C
g.2252A>C

AA changes

T4P Score: 38 explain score(s)

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

frameshift

known variant

Reference ID: rs2270641

database	homozygous (G/G)	heterozygous	allele carriers
1000G	186	861	1047
ExAC	2923	12346	15269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.278	0
	0.239	0.003
(flanking)	1.129	0.02

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	2261	wt: 0.26 / mu: 0.73	wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG	ctgg\|ATGC
Acc increased	2246	wt: 0.24 / mu: 0.36	wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT	atgc\|TCCG
Acc gained	2259	0.51	mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC	ttct\|GGAT

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000020039

Mmulatta

all identical

ENSMMUG00000019999

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000036330

Ggallus

no alignment

ENSGALG00000001693

n/a

Trubripes

no alignment

ENSTRUG00000012619

n/a

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0260964

n/a

Celegans

no alignment

W01C8.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	21	TOPO_DOM	Cytoplasmic (Potential).	lost
22	42	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
43	138	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
58	58	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
87	87	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
104	104	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
139	158	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
159	167	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
168	188	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
189	197	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
219	227	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
228	250	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
251	256	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
257	279	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	299	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
300	319	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
320	335	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
336	360	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
361	365	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
366	386	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
387	397	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
398	418	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
419	422	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
423	443	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
444	448	TOPO_DOM	Lumenal, vesicle (Potential).	might get lost (downstream of altered splice site)
449	470	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
471	525	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

1419 / 1419

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

473 / 473

position of stopcodon in wt / mu cDNA

1890 / 1890

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

472 / 472

chromosome

strand

-1

last intron/exon boundary

1802

theoretical NMD boundary in CDS

1280

length of CDS

1419

coding sequence (CDS) position

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

481

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

2252

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

20038466

original gDNA sequence snippet

CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG

altered gDNA sequence snippet

CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG

original cDNA sequence snippet

CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG

altered cDNA sequence snippet

CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG

wildtype AA sequence

MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*

mutated AA sequence

MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*

speed

1.02 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