mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.111954842650821 (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

ENST00000359865

Genbank transcript ID

NM_015210

UniProt peptide

Q9Y4B5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.725T>C
cDNA.867T>C
g.78177T>C

AA changes

M242T Score: 81 explain score(s)

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

242

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

242

mutated

not conserved

242

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
42	319	COMPBIAS	Pro-rich.	lost
330	404	COILED	Potential.	might get lost (downstream of altered splice site)
432	432	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
432	483	COILED	Potential.	might get lost (downstream of altered splice site)
513	718	COILED	Potential.	might get lost (downstream of altered splice site)
549	549	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
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

4761 / 4761

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

1587 / 1587

position of stopcodon in wt / mu cDNA

4903 / 4903

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

143 / 143

chromosome

strand

last intron/exon boundary

4922

theoretical NMD boundary in CDS

4729

length of CDS

4761

coding sequence (CDS) position

725

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

867

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

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 GGQTCFSLEL RGPPVLPEQS VSIEELQGQL VQAARLHQEE
TETFTNKIHK MEEEHLYALR WKELEMHSLA LQNTLHERTW SDEKNLMQQE LRSLKQNIFL
FYVKLRWLLK HWRQGKQMEE EGEEFTEGEH PETLSRLGEL GVQGGHQADG PDHDSDRGCG
FPVGEHSPHS RVQIGDHSLR LQTADRGQPH KQVVENQQLF SAFKALLEDF RAELREDERA
RLRLQQQYAS DKAAWDVEWA VLKCRLEQLE EKTENKLGEL GSSAESKGAL KKEREVHQKL
LADSHSLVMD LRWQIHHSEK NWNREKVELL DRLDRDRQEW ERQKKEFLWR IEQLQKENSP
RRGGSFLCDQ KDGNVRPFPH QGSLRMPRPV AMWPCADADS IPFEDRPLSK LKESDRCSAS
ENLYLDALSL DDEPEEPPAH RPEREFRNRL PEEEENHKGN LQRAVSVSSM SEFQRLMDIS
PFLPEKGLPS TSSKEDVTPP LSPDDLKYIE EFNKSWDYTP NRGHNGGGPD LWADRTEVGR
AGHEDSTEPF PDSSWYLTTS VTMTTDTMTS PEHCQKQPLR SHVLTEQSGL RVLHSPPAVR
RVDSITAAGG EGPFPTSRAR GSPGDTKGGP PEPMLSRWPC TSPRHSRDYV EGARRPLDSP
LCTSLGFASP LHSLEMSKNL SDDMKEVAFS VRNAICSGPG ELQVKDMACQ TNGSRTMGTQ
TVQTISVGLQ TEALRGSGVT SSPHKCLTPK AGGGATPVSS PSRSLRSRQV APAIEKVQAK
FERTCCSPKY GSPKLQRKPL PKADQPNNRT SPGMAQKGYS ESAWARSTTT RESPVHTTIN
DGLSSLFNII DHSPVVQDPF QKGLRAGSRS RSAEPRPELG PGQETGTNSR GRSPSPIGVG
SEMCREEGGE GTPVKQDLSA PPGYTLTENV ARILNKKLLE HALKEERRQA AHGPPGLHSD
SHSLGDTAEP GPMENQTVLL TAPWGL*

mutated AA sequence

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 GGQTCFSLEL RGPPVLPEQS VSIEELQGQL VQAARLHQEE
TETFTNKIHK MEEEHLYALR WKELEMHSLA LQNTLHERTW SDEKNLMQQE LRSLKQNIFL
FYVKLRWLLK HWRQGKQMEE EGEEFTEGEH PETLSRLGEL GVQGGHQADG PDHDSDRGCG
FPVGEHSPHS RVQIGDHSLR LQTADRGQPH KQVVENQQLF SAFKALLEDF RAELREDERA
RLRLQQQYAS DKAAWDVEWA VLKCRLEQLE EKTENKLGEL GSSAESKGAL KKEREVHQKL
LADSHSLVMD LRWQIHHSEK NWNREKVELL DRLDRDRQEW ERQKKEFLWR IEQLQKENSP
RRGGSFLCDQ KDGNVRPFPH QGSLRMPRPV AMWPCADADS IPFEDRPLSK LKESDRCSAS
ENLYLDALSL DDEPEEPPAH RPEREFRNRL PEEEENHKGN LQRAVSVSSM SEFQRLMDIS
PFLPEKGLPS TSSKEDVTPP LSPDDLKYIE EFNKSWDYTP NRGHNGGGPD LWADRTEVGR
AGHEDSTEPF PDSSWYLTTS VTMTTDTMTS PEHCQKQPLR SHVLTEQSGL RVLHSPPAVR
RVDSITAAGG EGPFPTSRAR GSPGDTKGGP PEPMLSRWPC TSPRHSRDYV EGARRPLDSP
LCTSLGFASP LHSLEMSKNL SDDMKEVAFS VRNAICSGPG ELQVKDMACQ TNGSRTMGTQ
TVQTISVGLQ TEALRGSGVT SSPHKCLTPK AGGGATPVSS PSRSLRSRQV APAIEKVQAK
FERTCCSPKY GSPKLQRKPL PKADQPNNRT SPGMAQKGYS ESAWARSTTT RESPVHTTIN
DGLSSLFNII DHSPVVQDPF QKGLRAGSRS RSAEPRPELG PGQETGTNSR GRSPSPIGVG
SEMCREEGGE GTPVKQDLSA PPGYTLTENV ARILNKKLLE HALKEERRQA AHGPPGLHSD
SHSLGDTAEP GPMENQTVLL TAPWGL*

speed

1.06 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