mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.0865730001018313 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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)

chr18:8783835T>CN/A show variant in all transcripts IGV

HGNC symbol

MTCL1

Ensembl transcript ID

ENST00000306329

Genbank transcript ID

N/A

UniProt peptide

Q9Y4B5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1805T>C
cDNA.1805T>C
g.78177T>C

AA changes

M602T Score: 81 explain score(s)

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

602

frameshift

known variant

Reference ID: rs35739383

database	homozygous (C/C)	heterozygous	allele carriers
1000G	508	1046	1554
ExAC	16968	-1169	15799

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.429	0.352
	5.099	0.999
(flanking)	1.185	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
Donor increased	78177	wt: 0.24 / mu: 0.59	wt: GGACATGCGGGGCCA mu: GGACACGCGGGGCCA	ACAT\|gcgg
Donor marginally increased	78172	wt: 0.9454 / mu: 0.9811 (marginal change - not scored)	wt: ATGGAGGACATGCGG mu: ATGGAGGACACGCGG	GGAG\|gaca

distance from splice site

308

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

602

mutated

not conserved

602

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000015761

275

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000052105

594

Ggallus

all identical

ENSGALG00000013357

242

Trubripes

all conserved

ENSTRUG00000008561

264

Drerio

all conserved

ENSDARG00000091408

492

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
513	718	COILED	Potential.	lost
618	618	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
621	621	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
622	622	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
685	685	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
749	749	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
776	776	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
907	907	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
923	923	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1143	1201	COILED	Potential.	might get lost (downstream of altered splice site)
1238	1278	COILED	Potential.	might get lost (downstream of altered splice site)
1385	1385	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1388	1388	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1417	1417	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1421	1421	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1427	1427	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
1514	1514	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1561	1561	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1578	1578	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1583	1583	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1588	1588	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1592	1592	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1661	1661	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1667	1667	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1675	1675	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1679	1679	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1681	1681	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1683	1683	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1812	1812	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1814	1814	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5718 / 5718

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

1906 / 1906

position of stopcodon in wt / mu cDNA

5718 / 5718

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

1 / 1

chromosome

strand

last intron/exon boundary

5680

theoretical NMD boundary in CDS

5629

length of CDS

5718

coding sequence (CDS) position

1805

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

1805

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

78177

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

8783835

original gDNA sequence snippet

CAAGGCAGAGATGGAGGACATGCGGGGCCAGCAGGAGCGGG

altered gDNA sequence snippet

CAAGGCAGAGATGGAGGACACGCGGGGCCAGCAGGAGCGGG

original cDNA sequence snippet

CAAGGCAGAGATGGAGGACATGCGGGGCCAGCAGGAGCGGG

altered cDNA sequence snippet

CAAGGCAGAGATGGAGGACACGCGGGGCCAGCAGGAGCGGG

wildtype AA sequence

METLNGPAGG GAPDAKLQPP GQHHRHHHLH PVAERRRLHR APSPARPFLK DLHARPAAPG
PAVPSSGRAP APAAPRSPNL AGKAPPSPGS LAAPGRLSRR SGGVPGAKDK PPPGAGARAA
GGAKAALGSR RAARVAPAEP LSRAGKPPGA EPPSAAAKGR KAKRGSRAPP ARTVGPPTPA
ARIPAVTLAV TSVAGSPARC SRISHTDSSS DLSDCPSEPL SDEQRLLPAA SSDAESGTGS
SDREPPRGAP TPSPAARGAP PGSPEPPALL AAPLAAGACP GGRSIPSGVS GGFAGPGVAE
DVRGRSPPER PVPGTPKEPS LGEQSRLVPA AEEEELLREM EELRSENDYL KDELDELRAE
MEEMRDSYLE EDVYQLQELR RELDRANKNC RILQYRLRKA EQKSLKVAET GQVDGELIRS
LEQDLKVAKD VSVRLHHELK TVEEKRAKAE DENETLRQQM IEVEISKQAL QNELERLKES
SLKRRSTREM YKEKKTFNQD DSADLRCQLQ FAKEEAFLMR KKMAKLGREK DELEQELQKY
KSLYGDVDSP LPTGEAGGPP STREAELKLR LKLVEEEANI LGRKIVELEV ENRGLKAEME
DMRGQQEREG PGRDHAPSIP TSPFGDSLES STELRRHLQF VEEEAELLRR SISEIEDHNR
QLTHELSKFK FEPPREPGWL GEGASPGAGG GAPLQEELKS ARLQISELSG KVLKLQHENH
ALLSNIQRCD LAAHLGLRAP SPRDSDAESD AGKKESDGEE SRLPQPKREG PVGGESDSEE
MFEKTSGFGS GKPSEASEPC PTELLKARED SEYLVTLKHE AQRLERTVER LITDTDSFLH
DAGLRGGAPL PGPGLQGEEE QGEGDQQEPQ LLGTINAKMK AFKKELQAFL EQVNRIGDGL
SPLPHLTESS SFLSTVTSVS RDSPIGNLGK ELGPDLQSRL KEQLEWQLGP ARGDERESLR
LRAARELHRR ADGDTGSHGL GGQTCFSLEM EEEHLYALRW KELEMHSLAL QNTLHERTWS
DEKNLMQQEL RSLKQNIFLF YVKLRWLLKH WRQGKQMEEE GEEFTEGEHP ETLSRLGELG
VQGGHQADGP DHDSDRGCGF PVGEHSPHSR VQIGDHSLRL QTADRGQPHK QVVENQQLFS
AFKALLEDFR AELREDERAR LRLQQQYASD KAAWDVEWAV LKCRLEQLEE KTENKLGELG
SSAESKGALK KEREVHQKLL ADSHSLVMDL RWQIHHSEKN WNREKVELLD RLDRDRQEWE
RQKKEFLWRI EQLQKENSPR RGGSFLCDQK DGNVRPFPHQ GSLRMPRPVA MWPCADADSI
PFEDRPLSKL KESDRCSASE NLYLDALSLD DEPEEPPAHR PEREFRNRLP EEEENHKGNL
QRAVSVSSMS EFQRLMDISP FLPEKGLPST SSKEDVTPPL SPDDLKYIEE FNKSWDYTPN
RGHNGGGPDL WADRTEVGRA GHEDSTEPFP DSSWYLTTSV TMTTDTMTSP EHCQKQPLRS
HVLTEQSGLR VLHSPPAVRR VDSITAAGGE GPFPTSRARG SPGDTKGGPP EPMLSRWPCT
SPRHSRDYVE GARRPLDSPL CTSLGFASPL HSLEMSKNLS DDMKEVAFSV RNAICSGPGE
LQVKDMACQT NGSRTMGTQT VQTISVGLQT EALRGSGVTS SPHKCLTPKA GGGATPVSSP
SRSLRSRQVA PAIEKVQAKF ERTCCSPKYG SPKLQRKPLP KADQPNNRTS PGMAQKGYSE
SAWARSTTTR ESPVHTTIND GLSSLFNIID HSPVVQDPFQ KGLRAGSRSR SAEPRPELGP
GQETGTNSRG RSPSPIGVGS EMCREEGGEG TPVKQDLSAP PGYTLTENVA RILNKKLLEH
ALKEERRQAA HGPPGLHSDS HSLGDTAEPG PMENQTVLLT APWGL*

mutated AA sequence

METLNGPAGG GAPDAKLQPP GQHHRHHHLH PVAERRRLHR APSPARPFLK DLHARPAAPG
PAVPSSGRAP APAAPRSPNL AGKAPPSPGS LAAPGRLSRR SGGVPGAKDK PPPGAGARAA
GGAKAALGSR RAARVAPAEP LSRAGKPPGA EPPSAAAKGR KAKRGSRAPP ARTVGPPTPA
ARIPAVTLAV TSVAGSPARC SRISHTDSSS DLSDCPSEPL SDEQRLLPAA SSDAESGTGS
SDREPPRGAP TPSPAARGAP PGSPEPPALL AAPLAAGACP GGRSIPSGVS GGFAGPGVAE
DVRGRSPPER PVPGTPKEPS LGEQSRLVPA AEEEELLREM EELRSENDYL KDELDELRAE
MEEMRDSYLE EDVYQLQELR RELDRANKNC RILQYRLRKA EQKSLKVAET GQVDGELIRS
LEQDLKVAKD VSVRLHHELK TVEEKRAKAE DENETLRQQM IEVEISKQAL QNELERLKES
SLKRRSTREM YKEKKTFNQD DSADLRCQLQ FAKEEAFLMR KKMAKLGREK DELEQELQKY
KSLYGDVDSP LPTGEAGGPP STREAELKLR LKLVEEEANI LGRKIVELEV ENRGLKAEME
DTRGQQEREG PGRDHAPSIP TSPFGDSLES STELRRHLQF VEEEAELLRR SISEIEDHNR
QLTHELSKFK FEPPREPGWL GEGASPGAGG GAPLQEELKS ARLQISELSG KVLKLQHENH
ALLSNIQRCD LAAHLGLRAP SPRDSDAESD AGKKESDGEE SRLPQPKREG PVGGESDSEE
MFEKTSGFGS GKPSEASEPC PTELLKARED SEYLVTLKHE AQRLERTVER LITDTDSFLH
DAGLRGGAPL PGPGLQGEEE QGEGDQQEPQ LLGTINAKMK AFKKELQAFL EQVNRIGDGL
SPLPHLTESS SFLSTVTSVS RDSPIGNLGK ELGPDLQSRL KEQLEWQLGP ARGDERESLR
LRAARELHRR ADGDTGSHGL GGQTCFSLEM EEEHLYALRW KELEMHSLAL QNTLHERTWS
DEKNLMQQEL RSLKQNIFLF YVKLRWLLKH WRQGKQMEEE GEEFTEGEHP ETLSRLGELG
VQGGHQADGP DHDSDRGCGF PVGEHSPHSR VQIGDHSLRL QTADRGQPHK QVVENQQLFS
AFKALLEDFR AELREDERAR LRLQQQYASD KAAWDVEWAV LKCRLEQLEE KTENKLGELG
SSAESKGALK KEREVHQKLL ADSHSLVMDL RWQIHHSEKN WNREKVELLD RLDRDRQEWE
RQKKEFLWRI EQLQKENSPR RGGSFLCDQK DGNVRPFPHQ GSLRMPRPVA MWPCADADSI
PFEDRPLSKL KESDRCSASE NLYLDALSLD DEPEEPPAHR PEREFRNRLP EEEENHKGNL
QRAVSVSSMS EFQRLMDISP FLPEKGLPST SSKEDVTPPL SPDDLKYIEE FNKSWDYTPN
RGHNGGGPDL WADRTEVGRA GHEDSTEPFP DSSWYLTTSV TMTTDTMTSP EHCQKQPLRS
HVLTEQSGLR VLHSPPAVRR VDSITAAGGE GPFPTSRARG SPGDTKGGPP EPMLSRWPCT
SPRHSRDYVE GARRPLDSPL CTSLGFASPL HSLEMSKNLS DDMKEVAFSV RNAICSGPGE
LQVKDMACQT NGSRTMGTQT VQTISVGLQT EALRGSGVTS SPHKCLTPKA GGGATPVSSP
SRSLRSRQVA PAIEKVQAKF ERTCCSPKYG SPKLQRKPLP KADQPNNRTS PGMAQKGYSE
SAWARSTTTR ESPVHTTIND GLSSLFNIID HSPVVQDPFQ KGLRAGSRSR SAEPRPELGP
GQETGTNSRG RSPSPIGVGS EMCREEGGEG TPVKQDLSAP PGYTLTENVA RILNKKLLEH
ALKEERRQAA HGPPGLHSDS HSLGDTAEPG PMENQTVLLT APWGL*

speed

0.77 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