Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999465 (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) | chr10:123996976G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | TACC2 |
| Ensembl transcript ID | ENST00000369001 |
| Genbank transcript ID | N/A |
| UniProt peptide | O95359 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.1075G>A
cDNA.2546G>A
g.248288G>A |
| AA changes | A359T Score: 58 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 359 |
| frameshift | no |
| known variant | Reference ID: rs2295879
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 194 | 960 | 1154 |
| ExAC | 5843 | 21081 | 26924 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.891 | 0 | | -0.382 | 0.001 | | (flanking) | 3.684 | 0.031 |
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 | 248278 | wt: 0.55 / mu: 0.61 | wt: AAAACAGCCTTGTACTCCCGCATCGGGACCGCTGAGGTGGA
mu: AAAACAGCCTTGTACTCCCGCATCGGGACCACTGAGGTGGA | ccgc|ATCG | | Acc marginally increased | 248282 | wt: 0.8313 / mu: 0.8516 (marginal change - not scored) | wt: CAGCCTTGTACTCCCGCATCGGGACCGCTGAGGTGGAGAAA
mu: CAGCCTTGTACTCCCGCATCGGGACCACTGAGGTGGAGAAA | atcg|GGAC | | Donor increased | 248288 | wt: 0.40 / mu: 0.91 | wt: GGACCGCTGAGGTGG
mu: GGACCACTGAGGTGG | ACCG|ctga | | Donor marginally increased | 248293 | wt: 0.9307 / mu: 0.9811 (marginal change - not scored) | wt: GCTGAGGTGGAGAAA
mu: ACTGAGGTGGAGAAA | TGAG|gtgg | | Donor gained | 248290 | 0.44 | mu: ACCACTGAGGTGGAG | CACT|gagg |
|
| distance from splice site | 67 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 359 | S | K | T | A | L | Y | S | R | I | G | T | A | E | V | E | K | P | A | G | L | L | F | Q | Q |
| mutated | not conserved | | 359 | S | K | T | A | L | Y | S | R | I | G | T | T | E | V | E | K | P | A | G | L | L | F | Q |
| Ptroglodytes | not conserved | ENSPTRG00000003008 | 2638 | S | A | D | A | L | L | S | R | L | A | H | P | A | S | L | C | G | A | L | D | Y | L | E |
| Mmulatta | not conserved | ENSMMUG00000013033 | 2637 | S | A | D | A | L | L | S | R | L | A | H | P | A | S | L | C | G | A | L | D | Y | L | E |
| Fcatus | all identical | ENSFCAG00000003650 | 2559 | C | G | A | L | D | Y | L | E | P | D | L | A | E | K | N | P | P | V | F | A | Q | K | L |
| Mmusculus | not conserved | ENSMUSG00000030852 | 2586 | S | R | L | AHPAS | L | C | G | A | L | G | Y | L | EPDL | A | E | K | N | P | P | V | F | A | Q |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000062790 | 1054 | S | K | G | S | L | Y | S | R | T | G | Y | I | E | G | E | S | P | - | | | | | |
| Dmelanogaster | not conserved | FBgn0026620 | 1079 | D | R | T | K | K | H | V | K | M | S | V | D | V | I | D | N | D | C | N | K | T | F | D |
| Celegans | no homologue | | | |
| Xtropicalis | not conserved | ENSXETG00000015587 | 743 | S | H | N | S | L | Y | S | R | T | V | A | M | | | | | | | | | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 482 | 549 | COMPBIAS | Pro-rich. | might get lost (downstream of altered splice site) | | 493 | 493 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 571 | 571 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 575 | 575 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 758 | 758 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 962 | 962 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1025 | 1025 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1267 | 1267 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1313 | 1313 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1426 | 1426 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 1562 | 1562 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1946 | 1946 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 1949 | 1949 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 1956 | 2016 | COMPBIAS | Pro-rich. | might get lost (downstream of altered splice site) | | 2072 | 2072 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2073 | 2073 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 2226 | 2226 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2246 | 2246 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 2256 | 2256 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2315 | 2403 | DOMAIN | SPAZ. | might get lost (downstream of altered splice site) | | 2317 | 2317 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2321 | 2321 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2359 | 2359 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2389 | 2389 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2390 | 2390 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2392 | 2392 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2394 | 2394 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2403 | 2403 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2420 | 2423 | COMPBIAS | Poly-Lys. | might get lost (downstream of altered splice site) | | 2512 | 2512 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 2675 | 2703 | COILED | Potential. | might get lost (downstream of altered splice site) | | 2746 | 2947 | COILED | Potential. | might get lost (downstream of altered splice site) | | 2884 | 2884 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 2896 | 2896 | CONFLICT | R -> Q (in Ref. 3; AAO62629/AAO62630). | might get lost (downstream of altered splice site) | | 2909 | 2909 | CONFLICT | S -> T (in Ref. 5; AAH39311). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1728 / 1728 |
| position (AA) of stopcodon in wt / mu AA sequence | 576 / 576 |
| position of stopcodon in wt / mu cDNA | 3199 / 3199 |
| 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 | 1472 / 1472 |
| chromosome | 10 |
| strand | 1 |
| last intron/exon boundary | 3134 |
| theoretical NMD boundary in CDS | 1612 |
| length of CDS | 1728 |
| coding sequence (CDS) position | 1075 |
cDNA position
(for ins/del: last normal base / first normal base) | 2546 |
gDNA position
(for ins/del: last normal base / first normal base) | 248288 |
chromosomal position
(for ins/del: last normal base / first normal base) | 123996976 |
| original gDNA sequence snippet | TGTACTCCCGCATCGGGACCGCTGAGGTGGAGAAACCTGCA |
| altered gDNA sequence snippet | TGTACTCCCGCATCGGGACCACTGAGGTGGAGAAACCTGCA |
| original cDNA sequence snippet | TGTACTCCCGCATCGGGACCGCTGAGGTGGAGAAACCTGCA |
| altered cDNA sequence snippet | TGTACTCCCGCATCGGGACCACTGAGGTGGAGAAACCTGCA |
| wildtype AA sequence | MPLRRPKMKK TPEKLDNTPA SPPRSPAEPN DIPIAKGTYT FDIDKWDDPN FNPFSSTSKM
QESPKLPQQS YNFDPDTCDE SVDPFKTSSK TPSSPSKSPA SFEIPASAME ANGVDGDGLN
KPAKKKKTPL KTDTFRVKKS PKRSPLSDPP SQDPTPAATP ETPPVISAVV HATDEEKLAV
TNQKWTCMTV DLEADKQDYP QPSDLSTFVN ETKFSSPTEE LDYRNSYEIE YMEKIGSSLP
QDDDAPKKQA LYLMFDTSQE SPVKSSPVRM SESPTPCSGS SFEETEALVN TAAKNQHPVP
RGLAPNQESH LQVPEKSSQK ELEAMGLGTP SEAIEIREAA HPTDVSISKT ALYSRIGTAE
VEKPAGLLFQ QPDLDSALQI ARAEIITKER EVSEWKDKYE ESRREVMEMR KIVAEYEKTI
AQMIEDEQRE KSVSHQTVQQ LVLEKEQALA DLNSVEKSLA DLFRRYEKMK EVLEGFRKNE
EVLKRCAQEY LSRVKKEEQR YQALKVHAEE KLDRANAEIA QVRGKAQQEQ AAHQASLRKE
QLRVDALERT LEQKNKEIEE LTKICDELIA KMGKS* |
| mutated AA sequence | MPLRRPKMKK TPEKLDNTPA SPPRSPAEPN DIPIAKGTYT FDIDKWDDPN FNPFSSTSKM
QESPKLPQQS YNFDPDTCDE SVDPFKTSSK TPSSPSKSPA SFEIPASAME ANGVDGDGLN
KPAKKKKTPL KTDTFRVKKS PKRSPLSDPP SQDPTPAATP ETPPVISAVV HATDEEKLAV
TNQKWTCMTV DLEADKQDYP QPSDLSTFVN ETKFSSPTEE LDYRNSYEIE YMEKIGSSLP
QDDDAPKKQA LYLMFDTSQE SPVKSSPVRM SESPTPCSGS SFEETEALVN TAAKNQHPVP
RGLAPNQESH LQVPEKSSQK ELEAMGLGTP SEAIEIREAA HPTDVSISKT ALYSRIGTTE
VEKPAGLLFQ QPDLDSALQI ARAEIITKER EVSEWKDKYE ESRREVMEMR KIVAEYEKTI
AQMIEDEQRE KSVSHQTVQQ LVLEKEQALA DLNSVEKSLA DLFRRYEKMK EVLEGFRKNE
EVLKRCAQEY LSRVKKEEQR YQALKVHAEE KLDRANAEIA QVRGKAQQEQ AAHQASLRKE
QLRVDALERT LEQKNKEIEE LTKICDELIA KMGKS* |
| speed | 1.70 s |
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