Prediction |
polymorphism |
Model: without_aae, prob: 2.71441763198242e-49 (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) | chr18:8783835T>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | MTCL1 |
| Ensembl transcript ID | ENST00000306285 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q9Y4B5 |
| alteration type | single base exchange |
| alteration region | 5'UTR |
| DNA changes | cDNA.867T>C
g.78177T>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| 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 | splice site change before start ATG (at aa -443) | | effect | gDNA position | score | 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? | no |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 42 | 319 | COMPBIAS | Pro-rich. | might get lost (downstream of altered splice site) | | 54 | 198 | COMPBIAS | Ala-rich. | might get lost (downstream of altered splice site) | | 87 | 87 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 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 | 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 | 2198 / 2198 |
| chromosome | 18 |
| strand | 1 |
| last intron/exon boundary | 4895 |
| theoretical NMD boundary in CDS | 2647 |
| length of CDS | 2931 |
| coding sequence (CDS) position | N/A |
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 | MHSLALQNTL HERTWSDEKN LMQQELRSLK QNIFLFYVKL RWLLKHWRQG KQMEEEGEEF
TEGEHPETLS RLGELGVQGG HQADGPDHDS DRGCGFPVGE HSPHSRVQIG DHSLRLQTAD
RGQPHKQVVE NQQLFSAFKA LLEDFRAELR EDERARLRLQ QQYASDKAAW DVEWAVLKCR
LEQNCCGYPR INIEEETLGF TRLPAGSTVK TLKSLGLQRL ELEEKTENKL GELGSSAESK
GALKKEREVH QKLLADSHSL VMDLRWQIHH SEKNWNREKV ELLDRLDRDR QEWERQKKEF
LWRIEQGSLR MPRPVAMWPC ADADSIPFED RPLSKLKESD RCSASENLYL DALSLDDEPE
EPPAHRPERE FRNRLPEEEE NHKGNLQRAV SVSSMSEFQR LMDISPFLPE KGLPSTSSKE
DVTPPLSPDD LKYIEEFNKS WDYTPNRGHN GGGPDLWADR TEVGRAGHED STEPFPDSSW
YLTTSVTMTT DTMTSPEHCQ KQPLRSHVLT EQSGLRVLHS PPAVRRVDSI TAAGGEGPFP
TSRARGSPGD TKGGPPEPML SRWPCTSPRH SRDYVEGARR PLDSPLCTSL GFASPLHSLE
MSKNLSDDMK EVAFSVRNAI CSGPGELQVK DMACQTNGSR TMGTQTVQTI SVGLQTEALR
GSGVTSSPHK CLTPKAGGGA TPVSSPSRSL RSRQVAPAIE KVQAKFERTC CSPKYGSPKL
QRKPLPKADQ PNNRTSPGMA QKGYSESAWA RSTTTRESPV HTTINDGLSS LFNIIDHSPV
VQDPFQKGLR AGSRSRSAEP RPELGPGQET GTNSRGRSPS PIGVGSEMCR EEGGEGTPVK
QDLSAPPGYT LTENVARILN KKLLEHALKE ERRQAAHGPP GLHSDSHSLG DTAEPGPMEE
LPCSALAPSL EPCFSRPERP ANRRPPSRWA PHSPTASQPQ SPGDPTSLEE HGGEEPPEEQ
PHRDASLHGL SQYNSL* |
| mutated AA sequence | N/A |
| speed | 0.84 s |
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