Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999777      (explain)
Summary
  • amino acid sequence changed
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:44374154C>TN/A show variant in all transcripts   IGV
HGNC symbol LRRC37A
Ensembl transcript ID ENST00000320254
Genbank transcript ID NM_014834
UniProt peptide A6NMS7
alteration type single base exchange
alteration region CDS
DNA changes c.1655C>T
cDNA.1658C>T
g.4056C>T
AA changes T552I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 552
frameshift no
known variant Variant was neither found in ExAC nor 1000G.
Search ExAC.
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.020
0.5230.001
(flanking)0.0580.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4067wt: 0.24 / mu: 0.35wt: TGGGGTTTACCATCACTCCAGAATCCAAGACAGAGGTTGAA
mu: TGGGGTTTATCATCACTCCAGAATCCAAGACAGAGGTTGAA		 ccag|AATC
Donor increased4061wt: 0.34 / mu: 0.40wt: CCATCACTCCAGAAT
mu: TCATCACTCCAGAAT		 ATCA|ctcc
distance from splice site 955
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      552QATVQPLDLGFTITPESKTEVELS
mutated  not conserved    552QATVQPLDLGFIITPESKTEVEL
Ptroglodytes  all identical  ENSPTRG00000009573  553QATVQPLDLGFTITPESMTEVEL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
361582TOPO_DOMExtracellular (Potential).lost
552552CONFLICTT -> I (in Ref. 1; CAH18088).lost
558558CONFLICTK -> M (in Ref. 1; CAH18088 and 3; AAH40501).might get lost (downstream of altered splice site)
630630CONFLICTP -> A (in Ref. 1; CAH18088 and 3; AAH40501).might get lost (downstream of altered splice site)
776776CONFLICTR -> H (in Ref. 1; CAH18088 and 3; AAH40501).might get lost (downstream of altered splice site)
785785CONFLICTR -> Q (in Ref. 1; CAH18088 and 3; AAH40501).might get lost (downstream of altered splice site)
866887REPEATLRR 1.might get lost (downstream of altered splice site)
890911REPEATLRR 2.might get lost (downstream of altered splice site)
914935REPEATLRR 3.might get lost (downstream of altered splice site)
938959REPEATLRR 4.might get lost (downstream of altered splice site)
965986REPEATLRR 5.might get lost (downstream of altered splice site)
10791079CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
12551255CONFLICTT -> A (in Ref. 1; CAH18088 and 3; AAH40501).might get lost (downstream of altered splice site)
12881288CONFLICTR -> G (in Ref. 1; CAH18088).might get lost (downstream of altered splice site)
13841384CONFLICTE -> G (in Ref. 3; AAH40501).might get lost (downstream of altered splice site)
15831603TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
16041700TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
16931693CONFLICTE -> G (in Ref. 3; AAH40501).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5103 / 5103
position (AA) of stopcodon in wt / mu AA sequence 1701 / 1701
position of stopcodon in wt / mu cDNA 5106 / 5106
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 4 / 4
chromosome 17
strand 1
last intron/exon boundary 5058
theoretical NMD boundary in CDS 5004
length of CDS 5103
coding sequence (CDS) position 1655
cDNA position
(for ins/del: last normal base / first normal base)		 1658
gDNA position
(for ins/del: last normal base / first normal base)		 4056
chromosomal position
(for ins/del: last normal base / first normal base)		 44374154
original gDNA sequence snippet ACCTTTGGATCTGGGGTTTACCATCACTCCAGAATCCAAGA
altered gDNA sequence snippet ACCTTTGGATCTGGGGTTTATCATCACTCCAGAATCCAAGA
original cDNA sequence snippet ACCTTTGGATCTGGGGTTTACCATCACTCCAGAATCCAAGA
altered cDNA sequence snippet ACCTTTGGATCTGGGGTTTATCATCACTCCAGAATCCAAGA
wildtype AA sequence MSSAQCPALV CVMSRLRFWG PWPLLMWQLL WLLVKEAQPL EWVKDPLQLT SNPLGPPESW
SSHSSHFPRE SPHAPTLPAD PWDFDHLGPS ASSEMPAPPQ ESTENLVPFL DTWDSAGEQP
LEPEQFLASQ QDLKDKLSPQ ERLPVSPKKL KKDPAQRWSL AEIIGITRQL STPQSQKQTL
QNEYSSTDTP YPGSLPPELR VKSDEPPGPS EQVGPSQFHL EPETQNPETL EDIQSSSLQQ
EAPAQLPQLL EEEPSSMQQE APALPPESSM ESLTLPNHEV SVQPPGEDQA YYHLPNITVK
PADVEVTITS EPTNETESSQ AQQETPIQFP EEVEPSATQQ EAPIEPPVPP MEHELSISEQ
QQPVQPSESP REVESSPTQQ ETPGQPPEHH EVTVSPPGHH QTHHLASPSV SVKPPDVQLT
IAAEPSAEVG TSLVHQEATT RLSGSGNDVE PPAIQHGGPP LLPESSEEAG PLAVQQETSF
QSPEPINNEN PSPTQQEAAA EHPQTAEEGE SSLTHQEAPA QTPEFPNVVV AQPPEHSHLT
QATVQPLDLG FTITPESKTE VELSPTMKET PTQPPKKVVP QLRVYQGVTN PTPGQDQAQH
PVSPSVTVQL LDLGLTITPE PTTEVGHSTP PKRTIVSPKH PEVTLPHPDQ VQTQHSHLTR
ATVQPLDLGF TITPKSMTEV EPSTALMTTA PPPGHPEVTL PPSDKGQAQH SHLTQATVQP
LDLELTITTK PTTEVKPSPT TEETSTQPPD LGLAIIPEPT TETGHSTALE KTTAPRPDRV
QTLHRSLTEV TGPPTELEPA QDSLVQSESY TQNKALTAPE EHKASTSTNI CELCTCGDEM
LSCIDLNPEQ RLRQVPVPEP NTHNGTFTIL NFQGNYISYI DGNVWKAYSW TEKLILRENN
LTELHKDSFE GLLSLQYLDL SCNKIQSIER HTFEPLPFLK FINLSCNVIT ELSFGTFQAW
HGMQFLHKLI LNHNPLTTVE DPYLFKLPAL KYLDMGTTLV PLTTLKNILM MTVELEKLIL
PSHMACCLCQ FKNSIEAVCK TVKLHCNSAC LTNTTHCPEE ASVGNPEGAF MKVLQARKNY
TSTELIVEPE EPSDSSGINL SGFGSEQLDT NDESDFISTL SYILPYFSAV NLDVKSLLLP
FIKLPTTGNS LAKIQTVGQN RQRVKRVLMG PRSIQKRHFK EVGRQSIRRE QGAQASVENA
AEEKRLTSPA PREVEQPHTQ QGPEKLAGNA VYTKPSFTQE HKAAVSVLKP FSKGTPSTSS
PAKALPQVRD RSKDLTHAIS ILESAKARVT NTKTSKPIVH ARKKYRFHKT RSHVTHRTTK
VKKSPKVRKK SYLSRLMLAN RLPFSAAKSL INSPSQGAFS SLGDLSPQEN PFLEVSALSE
HFIEKNNTKH TTARNAFEEN DFMENTNMPE GTISENTNYN HPPEADSAGT AFNLGPTVKQ
TETKWEYNNV GTDLSPEPKS FNYPLLSSPG DQFEIQLTQQ LQSLIPNNNV RRLIAHVIRT
LKMDCSGAHV QVTCAKLISR TGHLMKLLSG QQEVKASKIE WDTDQWKIEN YINESTEAQS
EQKEKSLELK KEVPGYGYTD KLILALIVTG ILTILIILFC LIVICCHRRS LQEDEEGFSR
GIFRFLPWRG CSSRRESQDG LSSFGQPLWF KDLYKPLSAT RINNHAWKLH KKSSNEDKIL
NRDPGDSEAP TEEEESEALP *
mutated AA sequence MSSAQCPALV CVMSRLRFWG PWPLLMWQLL WLLVKEAQPL EWVKDPLQLT SNPLGPPESW
SSHSSHFPRE SPHAPTLPAD PWDFDHLGPS ASSEMPAPPQ ESTENLVPFL DTWDSAGEQP
LEPEQFLASQ QDLKDKLSPQ ERLPVSPKKL KKDPAQRWSL AEIIGITRQL STPQSQKQTL
QNEYSSTDTP YPGSLPPELR VKSDEPPGPS EQVGPSQFHL EPETQNPETL EDIQSSSLQQ
EAPAQLPQLL EEEPSSMQQE APALPPESSM ESLTLPNHEV SVQPPGEDQA YYHLPNITVK
PADVEVTITS EPTNETESSQ AQQETPIQFP EEVEPSATQQ EAPIEPPVPP MEHELSISEQ
QQPVQPSESP REVESSPTQQ ETPGQPPEHH EVTVSPPGHH QTHHLASPSV SVKPPDVQLT
IAAEPSAEVG TSLVHQEATT RLSGSGNDVE PPAIQHGGPP LLPESSEEAG PLAVQQETSF
QSPEPINNEN PSPTQQEAAA EHPQTAEEGE SSLTHQEAPA QTPEFPNVVV AQPPEHSHLT
QATVQPLDLG FIITPESKTE VELSPTMKET PTQPPKKVVP QLRVYQGVTN PTPGQDQAQH
PVSPSVTVQL LDLGLTITPE PTTEVGHSTP PKRTIVSPKH PEVTLPHPDQ VQTQHSHLTR
ATVQPLDLGF TITPKSMTEV EPSTALMTTA PPPGHPEVTL PPSDKGQAQH SHLTQATVQP
LDLELTITTK PTTEVKPSPT TEETSTQPPD LGLAIIPEPT TETGHSTALE KTTAPRPDRV
QTLHRSLTEV TGPPTELEPA QDSLVQSESY TQNKALTAPE EHKASTSTNI CELCTCGDEM
LSCIDLNPEQ RLRQVPVPEP NTHNGTFTIL NFQGNYISYI DGNVWKAYSW TEKLILRENN
LTELHKDSFE GLLSLQYLDL SCNKIQSIER HTFEPLPFLK FINLSCNVIT ELSFGTFQAW
HGMQFLHKLI LNHNPLTTVE DPYLFKLPAL KYLDMGTTLV PLTTLKNILM MTVELEKLIL
PSHMACCLCQ FKNSIEAVCK TVKLHCNSAC LTNTTHCPEE ASVGNPEGAF MKVLQARKNY
TSTELIVEPE EPSDSSGINL SGFGSEQLDT NDESDFISTL SYILPYFSAV NLDVKSLLLP
FIKLPTTGNS LAKIQTVGQN RQRVKRVLMG PRSIQKRHFK EVGRQSIRRE QGAQASVENA
AEEKRLTSPA PREVEQPHTQ QGPEKLAGNA VYTKPSFTQE HKAAVSVLKP FSKGTPSTSS
PAKALPQVRD RSKDLTHAIS ILESAKARVT NTKTSKPIVH ARKKYRFHKT RSHVTHRTTK
VKKSPKVRKK SYLSRLMLAN RLPFSAAKSL INSPSQGAFS SLGDLSPQEN PFLEVSALSE
HFIEKNNTKH TTARNAFEEN DFMENTNMPE GTISENTNYN HPPEADSAGT AFNLGPTVKQ
TETKWEYNNV GTDLSPEPKS FNYPLLSSPG DQFEIQLTQQ LQSLIPNNNV RRLIAHVIRT
LKMDCSGAHV QVTCAKLISR TGHLMKLLSG QQEVKASKIE WDTDQWKIEN YINESTEAQS
EQKEKSLELK KEVPGYGYTD KLILALIVTG ILTILIILFC LIVICCHRRS LQEDEEGFSR
GIFRFLPWRG CSSRRESQDG LSSFGQPLWF KDLYKPLSAT RINNHAWKLH KKSSNEDKIL
NRDPGDSEAP TEEEESEALP *
speed 1.20 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