mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999892150588 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr22:44083442T>CN/A show variant in all transcripts IGV

HGNC symbol

EFCAB6

Ensembl transcript ID

ENST00000358439

Genbank transcript ID

N/A

UniProt peptide

Q5THR3

alteration type

single base exchange

alteration region

intron

DNA changes

g.124776A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs5764214

database	homozygous (C/C)	heterozygous	allele carriers
1000G	466	1150	1616
ExAC	11238	10291	21529

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.785	0
	-0.833	0.001
(flanking)	0.115	0.161

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 marginally increased	124769	wt: 0.9174 / mu: 0.9244 (marginal change - not scored)	wt: CTTAAAGCCACCACT mu: CTTAAAGCCACCGCT	TAAA\|gcca
Donor gained	124775	0.95	mu: GCCACCGCTAAAATC	CACC\|gcta

distance from splice site

9399

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
283	283	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
297	332	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)
403	438	DOMAIN	EF-hand 4.	might get lost (downstream of altered splice site)
439	474	DOMAIN	EF-hand 5.	might get lost (downstream of altered splice site)
478	478	CONFLICT	S -> P (in Ref. 2; BAF85187).	might get lost (downstream of altered splice site)
504	539	DOMAIN	EF-hand 6.	might get lost (downstream of altered splice site)
634	669	DOMAIN	EF-hand 7.	might get lost (downstream of altered splice site)
726	726	CONFLICT	I -> V (in Ref. 2; BAF85187).	might get lost (downstream of altered splice site)
741	776	DOMAIN	EF-hand 8.	might get lost (downstream of altered splice site)
754	765	CA_BIND	Potential.	might get lost (downstream of altered splice site)
833	833	CONFLICT	A -> V (in Ref. 2; BAF85187).	might get lost (downstream of altered splice site)
847	882	DOMAIN	EF-hand 9.	might get lost (downstream of altered splice site)
882	882	CONFLICT	P -> S (in Ref. 2; BAF85100).	might get lost (downstream of altered splice site)
883	918	DOMAIN	EF-hand 10.	might get lost (downstream of altered splice site)
964	999	DOMAIN	EF-hand 11.	might get lost (downstream of altered splice site)
990	990	CONFLICT	Q -> H (in Ref. 1; BAB71780 and 2; BAB15703).	might get lost (downstream of altered splice site)
1069	1104	DOMAIN	EF-hand 12.	might get lost (downstream of altered splice site)
1082	1082	CONFLICT	D -> G (in Ref. 5; AAH39315).	might get lost (downstream of altered splice site)
1139	1139	CONFLICT	E -> G (in Ref. 2; BAF85100).	might get lost (downstream of altered splice site)
1164	1176	HELIX		might get lost (downstream of altered splice site)
1176	1211	DOMAIN	EF-hand 13.	might get lost (downstream of altered splice site)
1178	1188	HELIX		might get lost (downstream of altered splice site)
1182	1182	CONFLICT	T -> P (in Ref. 2; BAF85187).	might get lost (downstream of altered splice site)
1198	1208	HELIX		might get lost (downstream of altered splice site)
1212	1247	DOMAIN	EF-hand 14.	might get lost (downstream of altered splice site)
1214	1221	HELIX		might get lost (downstream of altered splice site)
1218	1218	CONFLICT	D -> G (in Ref. 5; AAH39315).	might get lost (downstream of altered splice site)
1234	1241	HELIX		might get lost (downstream of altered splice site)
1303	1501	REGION	Interaction with PARK7.	might get lost (downstream of altered splice site)
1359	1394	DOMAIN	EF-hand 15.	might get lost (downstream of altered splice site)
1407	1501	REGION	Interaction with AR.	might get lost (downstream of altered splice site)
1434	1469	DOMAIN	EF-hand 16.	might get lost (downstream of altered splice site)
1470	1501	DOMAIN	EF-hand 17.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

184 / 184

chromosome

strand

-1

last intron/exon boundary

897

theoretical NMD boundary in CDS

663

length of CDS

732

coding sequence (CDS) position

N/A

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

N/A

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

124776

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

44083442

original gDNA sequence snippet

GATTTGGACTTAAAGCCACCACTAAAATCAATTGGAAGCAA

altered gDNA sequence snippet

GATTTGGACTTAAAGCCACCGCTAAAATCAATTGGAAGCAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVPQISSDLL QIPLSTSGTV PYLAFLSRFG GIDLYINGIK RGGGNEMNCC RTLRELEIQV
GEKVFKNIKT VMKAFELIDV NKTGLVRPQE LRRVLETFCM KLRDEEYEKF SKHYNIHKDT
AVDYNVFLKN LSINNDLNLR YCMGNQEVSL ENQQAKNSKK ERLLGSASSE DIWRNYSLDE
IERNFCLQLS KSYEKVEKAL SAGDPCKGGY VSFNYLKIVL DTFVYQIPRR IFIQLMKRNP
MDR*

mutated AA sequence

N/A

speed

0.65 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