Prediction |
disease causing |
Model: without_aae, prob: 1 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- known disease mutation at this position (HGMD CM092871)
- known disease mutation: rs6511 (pathogenic)
- protein features (might be) affected
- splice site changes
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hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr11:103033875A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | DYNC2H1 |
| Ensembl transcript ID | ENST00000334267 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q8NCM8 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.53716A>G |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs137853033
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs6511 (pathogenic for Short-rib thoracic dysplasia 3 with or without polydactyly) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM092871)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092871)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092871)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 5.123 | 1 | | 4.248 | 1 | | (flanking) | 2.594 | 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 | | Acc increased | 53709 | wt: 0.22 / mu: 0.39 | wt: CAGTTGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTT
mu: CAGTTGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTT | ttcc|CTTC | | Acc marginally increased | 53712 | wt: 0.6367 / mu: 0.6635 (marginal change - not scored) | wt: TTGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTACG
mu: TTGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTACG | cctt|CACA | | Acc marginally increased | 53721 | wt: 0.4351 / mu: 0.4658 (marginal change - not scored) | wt: CTCTGTTCCCTTCACAGGTAAGGGGGCTTACGTGTAGAAGC
mu: CTCTGTTCCCTTCACGGGTAAGGGGGCTTACGTGTAGAAGC | gtaa|GGGG | | Acc marginally increased | 53717 | wt: 0.9929 / mu: 0.9943 (marginal change - not scored) | wt: CCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTACGTGTAG
mu: CCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTACGTGTAG | acag|GTAA | | Acc increased | 53708 | wt: 0.23 / mu: 0.40 | wt: GCAGTTGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCT
mu: GCAGTTGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCT | gttc|CCTT | | Acc marginally increased | 53711 | wt: 0.6552 / mu: 0.6863 (marginal change - not scored) | wt: GTTGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTAC
mu: GTTGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTAC | ccct|TCAC | | Acc marginally increased | 53715 | wt: 0.9948 / mu: 0.9970 (marginal change - not scored) | wt: ACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTACGTGT
mu: ACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTACGTGT | tcac|AGGT | | Acc marginally increased | 53710 | wt: 0.8610 / mu: 0.8764 (marginal change - not scored) | wt: AGTTGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTA
mu: AGTTGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTA | tccc|TTCA | | Acc marginally increased | 53713 | wt: 0.8001 / mu: 0.8135 (marginal change - not scored) | wt: TGACCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTACGT
mu: TGACCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTACGT | cttc|ACAG | | Donor gained | 53710 | 0.36 | mu: GTTCCCTTCACGGGT | TCCC|ttca |
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| distance from splice site | 28727 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 1650 | REGION | Stem (By similarity). | might get lost (downstream of altered splice site) | | 1074 | 1103 | COILED | Potential. | might get lost (downstream of altered splice site) | | 1120 | 1120 | CONFLICT | I -> N (in Ref. 4; AAB09728). | might get lost (downstream of altered splice site) | | 1168 | 1168 | CONFLICT | D -> V (in Ref. 4; AAB09728). | might get lost (downstream of altered splice site) | | 1651 | 1875 | REGION | AAA 1 (By similarity). | might get lost (downstream of altered splice site) | | 1689 | 1696 | NP_BIND | ATP (Potential). | might get lost (downstream of altered splice site) | | 1784 | 1784 | CONFLICT | N -> H (in Ref. 6; CAB06054). | might get lost (downstream of altered splice site) | | 1864 | 1864 | CONFLICT | W -> Y (in Ref. 6; CAB06054). | might get lost (downstream of altered splice site) | | 1866 | 1867 | CONFLICT | LR -> FS (in Ref. 6; CAB06054). | might get lost (downstream of altered splice site) | | 1930 | 1930 | CONFLICT | E -> K (in Ref. 1; BAE46899). | might get lost (downstream of altered splice site) | | 1938 | 2161 | REGION | AAA 2 (By similarity). | might get lost (downstream of altered splice site) | | 1979 | 1986 | NP_BIND | ATP (Potential). | might get lost (downstream of altered splice site) | | 2251 | 2505 | REGION | AAA 3 (By similarity). | might get lost (downstream of altered splice site) | | 2291 | 2298 | NP_BIND | ATP (Potential). | might get lost (downstream of altered splice site) | | 2617 | 2863 | REGION | AAA 4 (By similarity). | might get lost (downstream of altered splice site) | | 2655 | 2662 | NP_BIND | ATP (Potential). | might get lost (downstream of altered splice site) | | 2881 | 3169 | REGION | Stalk (By similarity). | might get lost (downstream of altered splice site) | | 2897 | 2982 | COILED | Potential. | might get lost (downstream of altered splice site) | | 3095 | 3095 | CONFLICT | A -> V (in Ref. 7; CAD98012). | might get lost (downstream of altered splice site) | | 3109 | 3200 | COILED | Potential. | might get lost (downstream of altered splice site) | | 3244 | 3473 | REGION | AAA 5 (By similarity). | might get lost (downstream of altered splice site) | | 3408 | 3442 | COILED | Potential. | might get lost (downstream of altered splice site) | | 3665 | 3665 | CONFLICT | L -> P (in Ref. 7; CAD98012). | might get lost (downstream of altered splice site) | | 3690 | 3905 | REGION | AAA 6 (By similarity). | might get lost (downstream of altered splice site) | | 4258 | 4258 | CONFLICT | C -> R (in Ref. 3; BAB13905). | might get lost (downstream of altered splice site) |
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| 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 | 54 / 54 |
| chromosome | 11 |
| strand | 1 |
| last intron/exon boundary | 2658 |
| theoretical NMD boundary in CDS | 2554 |
| length of CDS | 2763 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | N/A |
gDNA position
(for ins/del: last normal base / first normal base) | 53716 |
chromosomal position
(for ins/del: last normal base / first normal base) | 103033875 |
| original gDNA sequence snippet | CCCATCTCTGTTCCCTTCACAGGTAAGGGGGCTTACGTGTA |
| altered gDNA sequence snippet | CCCATCTCTGTTCCCTTCACGGGTAAGGGGGCTTACGTGTA |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MANGTADVRK LFIFTTTQNY FGLMSELWDQ PLLCNCLEIN NFLDDGNQML LRVQRSDAGI
SFSNTIEFGD TKDKVLVFFK LRPEVITDEN LHDNILVSSM LESPISSLYQ AVRQVFAPML
LKDQEWSRNF DPKLQNLLSE LEAGLGIVLR RSDTNLTKLK FKEDDTRGIL TPSDEFQFWI
EQAHRGNKQI SKERANYFKE LFETIAREFY NLDSLSLLEV VDLVETTQDV VDDVWRQTEH
DHYPESRMLH LLDIIGGSFG RFVQKKLGTL NLWEDPYYLV KESLKAGISI CEQWVIVCNH
LTGQVWQRYV PHPWKNEKYF PETLDKLGKR LEEVLAIRTI HEKFLYFLPA SEEKIICLTR
VFEPFTGLNP VQYNPYTEPL WKAAVSQYEK IIAPAEQKIA GKLKNYISEI QDSPQQLLQA
FLKYKELVKR PTISKELMLE RETLLARLVD SIKDFRLDFE NRCRGIPGDA SGPLSGKNLS
EVVNSIVWVR QLELKVDDTI KIAEALLSDL PGFRCFHQSA KDLLDQLKLY EQEQFDDWSR
DIQSGLSDSR SGLCIEASSR IMELDSNDGL LKVHYSDRLV ILLREVRQLS ALGFVIPAKI
QQVANIAQKF CKQAIILKQV AHFYNSIDQQ MIQSQRPMML QSALAFEQII KNSKAGSGGK
SQITWDNPKE LEGYIQKLQN AAERLATENR KLRKWHTTFC EKVVVLMNID LLRQQQRWKD
GLQELRTGLA TVEAQCPLAW QSKWEGPEDP LQYLRGLVAR ALAIQNWVDK AEKQALLSET
LDLSELFHPD TFLNALRQET ARAVGRSVDS LKFVASWKGR LQEAKLQIKI SGLLLEGCSF
DGNQLSENQL DSPSVSSVLP CFMGWIPQDA CGPYSPDECI SLPVYTSAER DRVVTNIDVP
CGGNQDQWIQ CGAALFLKNQ * |
| mutated AA sequence | N/A |
| speed | 0.93 s |
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