mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.998966425206441 (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 CM034388)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:117199533G>AN/A show variant in all transcripts IGV

HGNC symbol

CFTR

Ensembl transcript ID

ENST00000454343

Genbank transcript ID

N/A

UniProt peptide

P13569

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1225G>A
cDNA.1357G>A
g.93696G>A

AA changes

V409M Score: 21 explain score(s)

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

409

frameshift

known variant

Reference ID: rs213950

database	homozygous (A/A)	heterozygous	allele carriers
1000G	962	991	1953
ExAC	15242	2283	17525

known disease mutation at this position, please check HGMD for details (HGMD ID CM034388)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.732	1
	0.952	1
(flanking)	3.204	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
Acc increased	93696	wt: 0.44 / mu: 0.50	wt: TCCAGACTTCACTTCTAATGGTGATTATGGGAGAACTGGAG mu: TCCAGACTTCACTTCTAATGATGATTATGGGAGAACTGGAG	atgg\|TGAT
Donor increased	93694	wt: 0.53 / mu: 0.74	wt: TCTAATGGTGATTAT mu: TCTAATGATGATTAT	TAAT\|ggtg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

409

mutated

all conserved

409

Ptroglodytes

not conserved

ENSPTRG00000019619

409

Mmulatta

not conserved

ENSMMUG00000011269

409

Fcatus

no alignment

ENSFCAG00000014955

n/a

Mmusculus

all conserved

ENSMUSG00000041301

450

KGEMLAITGSTGSGK

Ggallus

all conserved

ENSGALG00000009324

472

Trubripes

all conserved

ENSTRUG00000017143

437

KGKMLAVAGSTGAGK

Drerio

not conserved

ENSDARG00000041107

447

Dmelanogaster

not conserved

FBgn0038740

490

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000021796

471

protein features

start (aa)	end (aa)	feature	details
351	859	TOPO_DOM	Cytoplasmic (Potential).	lost
403	411	HELIX		lost
423	646	DOMAIN	ABC transporter 1.	might get lost (downstream of altered splice site)
433	436	HELIX		might get lost (downstream of altered splice site)
440	449	STRAND		might get lost (downstream of altered splice site)
453	457	STRAND		might get lost (downstream of altered splice site)
458	465	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
464	471	HELIX		might get lost (downstream of altered splice site)
478	484	STRAND		might get lost (downstream of altered splice site)
488	491	STRAND		might get lost (downstream of altered splice site)
499	501	STRAND		might get lost (downstream of altered splice site)
502	507	HELIX		might get lost (downstream of altered splice site)
514	523	HELIX		might get lost (downstream of altered splice site)
515	515	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
524	524	LIPID	S-palmitoyl cysteine.	might get lost (downstream of altered splice site)
527	530	HELIX		might get lost (downstream of altered splice site)
533	535	STRAND		might get lost (downstream of altered splice site)
536	538	HELIX		might get lost (downstream of altered splice site)
540	542	STRAND		might get lost (downstream of altered splice site)
550	563	HELIX		might get lost (downstream of altered splice site)
567	573	STRAND		might get lost (downstream of altered splice site)
574	577	TURN		might get lost (downstream of altered splice site)
580	589	HELIX		might get lost (downstream of altered splice site)
590	594	HELIX		might get lost (downstream of altered splice site)
595	597	TURN		might get lost (downstream of altered splice site)
598	603	STRAND		might get lost (downstream of altered splice site)
607	612	HELIX		might get lost (downstream of altered splice site)
614	620	STRAND		might get lost (downstream of altered splice site)
620	620	CONFLICT	H -> N (in Ref. 1; AAA35680).	might get lost (downstream of altered splice site)
623	628	STRAND		might get lost (downstream of altered splice site)
630	634	HELIX		might get lost (downstream of altered splice site)
640	644	HELIX		might get lost (downstream of altered splice site)
650	652	HELIX		might get lost (downstream of altered splice site)
655	669	HELIX		might get lost (downstream of altered splice site)
660	660	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
686	686	MOD_RES	Phosphoserine; by PKC.	might get lost (downstream of altered splice site)
688	688	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin).	might get lost (downstream of altered splice site)
700	700	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
712	712	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
717	717	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
737	737	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
753	753	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
768	768	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
790	790	MOD_RES	Phosphoserine; by PKC.	might get lost (downstream of altered splice site)
795	795	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
813	813	MOD_RES	Phosphoserine; by PKA.	might get lost (downstream of altered splice site)
833	833	CONFLICT	F -> L (in Ref. 1; AAA35680).	might get lost (downstream of altered splice site)
859	1155	DOMAIN	ABC transmembrane type-1 2.	might get lost (downstream of altered splice site)
860	880	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
881	911	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
894	894	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
900	900	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
912	932	TRANSMEM	Helical; Name=8; (Potential).	might get lost (downstream of altered splice site)
933	990	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
991	1011	TRANSMEM	Helical; Name=9; (Potential).	might get lost (downstream of altered splice site)
1012	1013	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1014	1034	TRANSMEM	Helical; Name=10; (Potential).	might get lost (downstream of altered splice site)
1035	1102	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1103	1123	TRANSMEM	Helical; Name=11; (Potential).	might get lost (downstream of altered splice site)
1124	1128	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1129	1149	TRANSMEM	Helical; Name=12; (Potential).	might get lost (downstream of altered splice site)
1150	1480	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1176	1176	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1204	1207	STRAND		might get lost (downstream of altered splice site)
1210	1223	STRAND		might get lost (downstream of altered splice site)
1210	1443	DOMAIN	ABC transporter 2.	might get lost (downstream of altered splice site)
1226	1234	STRAND		might get lost (downstream of altered splice site)
1239	1245	STRAND		might get lost (downstream of altered splice site)
1244	1251	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)
1250	1258	HELIX		might get lost (downstream of altered splice site)
1261	1271	STRAND		might get lost (downstream of altered splice site)
1279	1284	HELIX		might get lost (downstream of altered splice site)
1286	1290	STRAND		might get lost (downstream of altered splice site)
1297	1299	STRAND		might get lost (downstream of altered splice site)
1300	1304	HELIX		might get lost (downstream of altered splice site)
1312	1321	HELIX		might get lost (downstream of altered splice site)
1325	1328	HELIX		might get lost (downstream of altered splice site)
1334	1336	HELIX		might get lost (downstream of altered splice site)
1341	1345	TURN		might get lost (downstream of altered splice site)
1348	1361	HELIX		might get lost (downstream of altered splice site)
1366	1371	STRAND		might get lost (downstream of altered splice site)
1372	1375	HELIX		might get lost (downstream of altered splice site)
1378	1389	HELIX		might get lost (downstream of altered splice site)
1390	1394	TURN		might get lost (downstream of altered splice site)
1395	1395	LIPID	S-palmitoyl cysteine.	might get lost (downstream of altered splice site)
1397	1400	STRAND		might get lost (downstream of altered splice site)
1402	1404	STRAND		might get lost (downstream of altered splice site)
1405	1407	HELIX		might get lost (downstream of altered splice site)
1411	1417	STRAND		might get lost (downstream of altered splice site)
1420	1426	STRAND		might get lost (downstream of altered splice site)
1444	1444	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1456	1456	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1478	1480	STRAND		might get lost (downstream of altered splice site)
1478	1480	MOTIF	PDZ-binding.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4260 / 4260

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

1420 / 1420

position of stopcodon in wt / mu cDNA

4392 / 4392

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

133 / 133

chromosome

strand

last intron/exon boundary

4192

theoretical NMD boundary in CDS

4009

length of CDS

4260

coding sequence (CDS) position

1225

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

1357

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

93696

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

117199533

original gDNA sequence snippet

TCCAGACTTCACTTCTAATGGTGATTATGGGAGAACTGGAG

altered gDNA sequence snippet

TCCAGACTTCACTTCTAATGATGATTATGGGAGAACTGGAG

original cDNA sequence snippet

AGGAGACTTCACTTCTAATGGTGATTATGGGAGAACTGGAG

altered cDNA sequence snippet

AGGAGACTTCACTTCTAATGATGATTATGGGAGAACTGGAG

wildtype AA sequence

MQRSPLEKAS VVSKLFFSWT RPILRKGYRQ RLELSDIYQI PSVDSADNLS EKLEREWDRE
LASKKNPKLI NALRRCFFWR FMFYGIFLYL GEVTKAVQPL LLGRIIASYD PDNKEERSIA
IYLGIGLCLL FIVRTLLLHP AIFGLHHIGM QMRIAMFSLI YKKTLKLSSR VLDKISIGQL
VSLLSNNLNK FDEGLALAHF VWIAPLQVAL LMGLIWELLQ ASAFCGLGFL IVLALFQAGL
GRMMMKYRDQ RAGKISERLV ITSEMIENIQ SVKAYCWEEA MEKMIENLRQ TELKLTRKAA
YVRYFNSSAF FFSGFFVVFL SVLPYALIKG IILRKIFTTI SFCIVLRMAV TRQFPWAVQT
WYDSLGAINK IQDFLQKQEY KTLEYNLTTT EVVMENVTAF WEETSLLMVI MGELEPSEGK
IKHSGRISFC SQFSWIMPGT IKENIIFGVS YDEYRYRSVI KACQLEEDIS KFAEKDNIVL
GEGGITLSGG QRARISLARA VYKDADLYLL DSPFGYLDVL TEKEIFESCV CKLMANKTRI
LVTSKMEHLK KADKILILHE GSSYFYGTFS ELQNLQPDFS SKLMGCDSFD QFSAERRNSI
LTETLHRFSL EGDAPVSWTE TKKQSFKQTG EFGEKRKNSI LNPINSIRKF SIVQKTPLQM
NGIEEDSDEP LERRLSLVPD SEQGEAILPR ISVISTGPTL QARRRQSVLN LMTHSVNQGQ
NIHRKTTAST RKVSLAPQAN LTELDIYSRR LSQETGLEIS EEINEEDLKE CFFDDMESIP
AVTTWNTYLR YITVHKSLIF VLIWCLVIFL AEVAASLVVL WLLGNTPLQD KGNSTHSRNN
SYAVIITSTS SYYVFYIYVG VADTLLAMGF FRGLPLVHTL ITVSKILHHK MLHSVLQAPM
STLNTLKAGG ILNRFSKDIA ILDDLLPLTI FDFIQLLLIV IGAIAVVAVL QPYIFVATVP
VIVAFIMLRA YFLQTSQQLK QLESEGRSPI FTHLVTSLKG LWTLRAFGRQ PYFETLFHKA
LNLHTANWFL YLSTLRWFQM RIEMIFVIFF IAVTFISILT TGEGEGRVGI ILTLAMNIMS
TLQWAVNSSI DVDSLMRSVS RVFKFIDMPT EGKPTKSTKP YKNGQLSKVM IIENSHVKKD
DIWPSGGQMT VKDLTAKYTE GGNAILENIS FSISPGQRVG LLGRTGSGKS TLLSAFLRLL
NTEGEIQIDG VSWDSITLQQ WRKAFGVIPQ KVFIFSGTFR KNLDPYEQWS DQEIWKVADE
VGLRSVIEQF PGKLDFVLVD GGCVLSHGHK QLMCLARSVL SKAKILLLDE PSAHLDPVTY
QIIRRTLKQA FADCTVILCE HRIEAMLECQ QFLVIEENKV RQYDSIQKLL NERSLFRQAI
SPSDRVKLFP HRNSSKCKSK PQIAALKEET EEEVQDTRL*

mutated AA sequence

MQRSPLEKAS VVSKLFFSWT RPILRKGYRQ RLELSDIYQI PSVDSADNLS EKLEREWDRE
LASKKNPKLI NALRRCFFWR FMFYGIFLYL GEVTKAVQPL LLGRIIASYD PDNKEERSIA
IYLGIGLCLL FIVRTLLLHP AIFGLHHIGM QMRIAMFSLI YKKTLKLSSR VLDKISIGQL
VSLLSNNLNK FDEGLALAHF VWIAPLQVAL LMGLIWELLQ ASAFCGLGFL IVLALFQAGL
GRMMMKYRDQ RAGKISERLV ITSEMIENIQ SVKAYCWEEA MEKMIENLRQ TELKLTRKAA
YVRYFNSSAF FFSGFFVVFL SVLPYALIKG IILRKIFTTI SFCIVLRMAV TRQFPWAVQT
WYDSLGAINK IQDFLQKQEY KTLEYNLTTT EVVMENVTAF WEETSLLMMI MGELEPSEGK
IKHSGRISFC SQFSWIMPGT IKENIIFGVS YDEYRYRSVI KACQLEEDIS KFAEKDNIVL
GEGGITLSGG QRARISLARA VYKDADLYLL DSPFGYLDVL TEKEIFESCV CKLMANKTRI
LVTSKMEHLK KADKILILHE GSSYFYGTFS ELQNLQPDFS SKLMGCDSFD QFSAERRNSI
LTETLHRFSL EGDAPVSWTE TKKQSFKQTG EFGEKRKNSI LNPINSIRKF SIVQKTPLQM
NGIEEDSDEP LERRLSLVPD SEQGEAILPR ISVISTGPTL QARRRQSVLN LMTHSVNQGQ
NIHRKTTAST RKVSLAPQAN LTELDIYSRR LSQETGLEIS EEINEEDLKE CFFDDMESIP
AVTTWNTYLR YITVHKSLIF VLIWCLVIFL AEVAASLVVL WLLGNTPLQD KGNSTHSRNN
SYAVIITSTS SYYVFYIYVG VADTLLAMGF FRGLPLVHTL ITVSKILHHK MLHSVLQAPM
STLNTLKAGG ILNRFSKDIA ILDDLLPLTI FDFIQLLLIV IGAIAVVAVL QPYIFVATVP
VIVAFIMLRA YFLQTSQQLK QLESEGRSPI FTHLVTSLKG LWTLRAFGRQ PYFETLFHKA
LNLHTANWFL YLSTLRWFQM RIEMIFVIFF IAVTFISILT TGEGEGRVGI ILTLAMNIMS
TLQWAVNSSI DVDSLMRSVS RVFKFIDMPT EGKPTKSTKP YKNGQLSKVM IIENSHVKKD
DIWPSGGQMT VKDLTAKYTE GGNAILENIS FSISPGQRVG LLGRTGSGKS TLLSAFLRLL
NTEGEIQIDG VSWDSITLQQ WRKAFGVIPQ KVFIFSGTFR KNLDPYEQWS DQEIWKVADE
VGLRSVIEQF PGKLDFVLVD GGCVLSHGHK QLMCLARSVL SKAKILLLDE PSAHLDPVTY
QIIRRTLKQA FADCTVILCE HRIEAMLECQ QFLVIEENKV RQYDSIQKLL NERSLFRQAI
SPSDRVKLFP HRNSSKCKSK PQIAALKEET EEEVQDTRL*

speed

0.72 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