mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999983939 (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 CM025961)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:220502367A>CN/A show variant in all transcripts IGV

HGNC symbol

SLC4A3

Ensembl transcript ID

ENST00000273063

Genbank transcript ID

NM_201574

UniProt peptide

P48751

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2681A>C
cDNA.2895A>C
g.10319A>C

AA changes

D894A Score: 126 explain score(s)

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

894

frameshift

known variant

Reference ID: rs635311

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1176	1041	2217
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM025961)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.984	0.025
	-0.593	0
(flanking)	-0.047	0

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 gained	10324	0.48	mu: TGGAGGGGTCCCTGGCTGCTGGTCTGGAGCCAAATGGCAGT	gctg\|GTCT
Acc gained	10328	0.54	mu: GGGGTCCCTGGCTGCTGGTCTGGAGCCAAATGGCAGTGCCC	gtct\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

894

mutated

not conserved

894

Ptroglodytes

all identical

ENSPTRG00000012966

894

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000006669

894

Mmusculus

not conserved

ENSMUSG00000006576

866

Ggallus

not conserved

ENSGALG00000011224

888

Trubripes

not conserved

ENSTRUG00000002078

843

Drerio

not conserved

ENSDARG00000053678

816

Dmelanogaster

not conserved

FBgn0036043

890

YNLP

PTLVAH

LLNA

NITQMVMNI

Celegans

not conserved

R03E9.3

602

Xtropicalis

not conserved

ENSXETG00000007160

625

protein features

start (aa)	end (aa)	feature	details
709	1232	REGION	Membrane (anion exchange).	lost
893	910	TRANSMEM	Helical; (Potential).	lost
899	899	CONFLICT	L -> P (in Ref. 2; AAB05850).	might get lost (downstream of altered splice site)
911	925	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
926	946	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
953	953	CONFLICT	K -> N (in Ref. 4; BAF82663).	might get lost (downstream of altered splice site)
955	955	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
958	958	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
961	961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
980	1002	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
983	983	CONFLICT	P -> L (in Ref. 7; AAI71760).	might get lost (downstream of altered splice site)
1028	1049	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1052	1052	CONFLICT	R -> H (in Ref. 4; BAF82663).	might get lost (downstream of altered splice site)
1054	1054	CONFLICT	V -> I (in Ref. 3; AAN34939).	might get lost (downstream of altered splice site)
1083	1128	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1096	1096	CONFLICT	I -> M (in Ref. 2; AAB05850).	might get lost (downstream of altered splice site)
1155	1191	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1165	1165	LIPID	S-palmitoyl cysteine (By similarity).	might get lost (downstream of altered splice site)
1184	1187	COMPBIAS	Poly-Leu.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3780 / 3780

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

1260 / 1260

position of stopcodon in wt / mu cDNA

3994 / 3994

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

215 / 215

chromosome

strand

last intron/exon boundary

3917

theoretical NMD boundary in CDS

3652

length of CDS

3780

coding sequence (CDS) position

2681

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

2895

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

10319

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

220502367

original gDNA sequence snippet

GGCCCTGGAGGGGTCCCTGGATGCTGGTCTGGAGCCAAATG

altered gDNA sequence snippet

GGCCCTGGAGGGGTCCCTGGCTGCTGGTCTGGAGCCAAATG

original cDNA sequence snippet

GGCCCTGGAGGGGTCCCTGGATGCTGGTCTGGAGCCAAATG

altered cDNA sequence snippet

GGCCCTGGAGGGGTCCCTGGCTGCTGGTCTGGAGCCAAATG

wildtype AA sequence

MANGVIPPPG GASPLPQVRV PLEEPPLSPD VEEEDDDLGK TLAVSRFGDL ISKPPAWDPE
KPSRSYSERD FEFHRHTSHH THHPLSARLP PPHKLRRLPP TSARHTRRKR KKEKTSAPPS
EGTPPIQEEG GAGVDEEEEE EEEEEGESEA EPVEPPHSGT PQKAKFSIGS DEDDSPGLPG
RAAVTKPLPS VGPHTDKSPQ HSSRPCSELR DGDGTTDLAL SSPRLLCCLP SSPSPRARAS
RLAGEKSRPW SPSASYDLRE RLCPGSALGN PGGPEQQVPT DEAEAQMLGS ADLDDMKSHR
LEDNPGVRRH LVKKPSRTQG GRGSPSGLAP ILRRKKKKKK LDRRPHEVFV ELNELMLDRS
QEPHWRETAR WIKFEEDVEE ETERWGKPHV ASLSFRSLLE LRRTIAHGAA LLDLEQTTLP
GIAHLVVETM IVSDQIRPED RASVLRTLLL KHSHPNDDKD SGFFPRNPSS SSMNSVLGNH
HPTPSHGPDG AVPTMADDLG EPAPLWPHDP DAKEKPLHMP GGDGHRGKSL KLLEKIPEDA
EATVVLVGCV PFLEQPAAAF VRLNEAVLLE SVLEVPVPVR FLFVMLGPSH TSTDYHELGR
SIATLMSDKL FHEAAYQADD RQDLLSAISE FLDGSIVIPP SEVEGRDLLR SVAAFQRELL
RKRREREQTK VEMTTRGGYT APGKELSLEL GGSEATPEDD PLLRTGSVFG GLVRDVRRRY
PHYPSDLRDA LHSQCVAAVL FIYFAALSPA ITFGGLLGEK TEGLMGVSEL IVSTAVLGVL
FSLLGAQPLL VVGFSGPLLV FEEAFFKFCR AQDLEYLTGR VWVGLWLVVF VLALVAAEGS
FLVRYISPFT QEIFAFLISL IFIYETFYKL YKVFTEHPLL PFYPPEGALE GSLDAGLEPN
GSALPPTEGP PSPRNQPNTA LLSLILMLGT FFIAFFLRKF RNSRFLGGKA RRIIGDFGIP
ISILVMVLVD YSITDTYTQK LTVPTGLSVT SPDKRSWFIP PLGSARPFPP WMMVAAAVPA
LLVLILIFME TQITALIVSQ KARRLLKGSG FHLDLLLIGS LGGLCGLFGL PWLTAATVRS
VTHVNALTVM RTAIAPGDKP QIQEVREQRV TGVLIASLVG LSIVMGAVLR RIPLAVLFGI
FLYMGVTSLS GIQLSQRLLL ILMPAKHHPE QPYVTKVKTW RMHLFTCIQL GCIALLWVVK
STAASLAFPF LLLLTVPLRH CLLPRLFQDR ELQALDSEDA EPNFDEDGQD EYNELHMPV*

mutated AA sequence

MANGVIPPPG GASPLPQVRV PLEEPPLSPD VEEEDDDLGK TLAVSRFGDL ISKPPAWDPE
KPSRSYSERD FEFHRHTSHH THHPLSARLP PPHKLRRLPP TSARHTRRKR KKEKTSAPPS
EGTPPIQEEG GAGVDEEEEE EEEEEGESEA EPVEPPHSGT PQKAKFSIGS DEDDSPGLPG
RAAVTKPLPS VGPHTDKSPQ HSSRPCSELR DGDGTTDLAL SSPRLLCCLP SSPSPRARAS
RLAGEKSRPW SPSASYDLRE RLCPGSALGN PGGPEQQVPT DEAEAQMLGS ADLDDMKSHR
LEDNPGVRRH LVKKPSRTQG GRGSPSGLAP ILRRKKKKKK LDRRPHEVFV ELNELMLDRS
QEPHWRETAR WIKFEEDVEE ETERWGKPHV ASLSFRSLLE LRRTIAHGAA LLDLEQTTLP
GIAHLVVETM IVSDQIRPED RASVLRTLLL KHSHPNDDKD SGFFPRNPSS SSMNSVLGNH
HPTPSHGPDG AVPTMADDLG EPAPLWPHDP DAKEKPLHMP GGDGHRGKSL KLLEKIPEDA
EATVVLVGCV PFLEQPAAAF VRLNEAVLLE SVLEVPVPVR FLFVMLGPSH TSTDYHELGR
SIATLMSDKL FHEAAYQADD RQDLLSAISE FLDGSIVIPP SEVEGRDLLR SVAAFQRELL
RKRREREQTK VEMTTRGGYT APGKELSLEL GGSEATPEDD PLLRTGSVFG GLVRDVRRRY
PHYPSDLRDA LHSQCVAAVL FIYFAALSPA ITFGGLLGEK TEGLMGVSEL IVSTAVLGVL
FSLLGAQPLL VVGFSGPLLV FEEAFFKFCR AQDLEYLTGR VWVGLWLVVF VLALVAAEGS
FLVRYISPFT QEIFAFLISL IFIYETFYKL YKVFTEHPLL PFYPPEGALE GSLAAGLEPN
GSALPPTEGP PSPRNQPNTA LLSLILMLGT FFIAFFLRKF RNSRFLGGKA RRIIGDFGIP
ISILVMVLVD YSITDTYTQK LTVPTGLSVT SPDKRSWFIP PLGSARPFPP WMMVAAAVPA
LLVLILIFME TQITALIVSQ KARRLLKGSG FHLDLLLIGS LGGLCGLFGL PWLTAATVRS
VTHVNALTVM RTAIAPGDKP QIQEVREQRV TGVLIASLVG LSIVMGAVLR RIPLAVLFGI
FLYMGVTSLS GIQLSQRLLL ILMPAKHHPE QPYVTKVKTW RMHLFTCIQL GCIALLWVVK
STAASLAFPF LLLLTVPLRH CLLPRLFQDR ELQALDSEDA EPNFDEDGQD EYNELHMPV*

speed

0.55 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