Prediction |
polymorphism |
Model: simple_aae, prob: 0.0246758514292884 (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
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr13:25831888T>CN/A
show variant in all transcripts IGV
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HGNC symbol | MTMR6 |
Ensembl transcript ID | ENST00000540661 |
Genbank transcript ID | N/A |
UniProt peptide | Q9Y217 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.955A>G cDNA.1274A>G g.30260A>G |
AA changes | I319V Score: 29 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 319 |
frameshift | no |
known variant | Reference ID: rs7995033
database | homozygous (C/C) | heterozygous | allele carriers |
1000G | 766 | 933 | 1699 |
ExAC | 32111 | -31455 | 656 |
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 2.951 | 1 | | 0.515 | 0.999 | (flanking) | 0.347 | 0.998 | 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 | 30268 | wt: 0.30 / mu: 0.41 | wt: ATGGATGCTGCAATCTTCTTGGCCAAAGTAATACTTTATCT mu: ATGGATGCTGCAGTCTTCTTGGCCAAAGTAATACTTTATCT | cttg|GCCA |
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distance from splice site | 15 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 319 | L | R | H | I | K | A | V | M | D | A | A | I | F | L | A | K | A | I | T | V | E | N | A | S |
mutated | all conserved | | 319 | L | R | H | I | K | A | V | M | D | A | A | V | F | L | A | K | A | I | T | V | E | N | A |
Ptroglodytes | all identical | ENSPTRG00000005718 | 319 | L | R | H | I | K | A | V | M | D | A | A | I | F | L | A | K | A | I | T | V | E | N | A |
Mmulatta | all identical | ENSMMUG00000018419 | 319 | L | R | H | I | K | A | V | M | D | A | A | I | F | L | A | K | A | I | T | V | E | N | A |
Fcatus | all identical | ENSFCAG00000010195 | 319 | L | R | H | I | K | A | V | M | D | A | A | I | F | L | A | K | A | I | T | V | E | S | A |
Mmusculus | all identical | ENSMUSG00000021987 | 319 | L | R | H | I | K | A | V | L | D | A | A | I | F | L | A | K | A | I | V | V | E | N | A |
Ggallus | all conserved | ENSGALG00000017112 | 319 | L | R | H | I | K | A | V | L | D | A | A | V | F | L | V | K | A | I | A | V | E | S | A |
Trubripes | all conserved | ENSTRUG00000001228 | 324 | L | R | H | I | K | A | V | V | DNL | D | L | V | F | C | S | K | A | V | T | G | E | G | A |
Drerio | all identical | ENSDARG00000016794 | 320 | L | R | H | I | K | A | I | M | D | A | A | I | F | L | A | K | A | V | S | V | E | G | A |
Dmelanogaster | not conserved | FBgn0028497 | 390 | L | K | H | I | R | S | I | L | D | T | S | S | F | I | A | N | A | V | D | - | K | G | V |
Celegans | all conserved | F53A2.8 | 425 | L | K | H | V | R | S | V | V | E | C | S | L | F | L | A | E | S | I | S | - | R | G | T |
Xtropicalis | no homologue | | | |
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protein features | start (aa) | end (aa) | feature | details | | 124 | 499 | DOMAIN | Myotubularin phosphatase. | lost | 307 | 326 | HELIX | | lost | 332 | 334 | STRAND | | might get lost (downstream of altered splice site) | 333 | 333 | CONFLICT | L -> S (in Ref. 2; AAL01037 and 7; AAC78841). | might get lost (downstream of altered splice site) | 336 | 336 | ACT_SITE | Phosphocysteine intermediate (By similarity). | might get lost (downstream of altered splice site) | 336 | 338 | TURN | | might get lost (downstream of altered splice site) | 336 | 342 | REGION | Substrate binding (By similarity). | might get lost (downstream of altered splice site) | 339 | 341 | STRAND | | might get lost (downstream of altered splice site) | 342 | 354 | HELIX | | might get lost (downstream of altered splice site) | 357 | 359 | HELIX | | might get lost (downstream of altered splice site) | 361 | 371 | HELIX | | might get lost (downstream of altered splice site) | 368 | 368 | CONFLICT | I -> T (in Ref. 3; BAG37162). | might get lost (downstream of altered splice site) | 372 | 376 | TURN | | might get lost (downstream of altered splice site) | 379 | 383 | HELIX | | might get lost (downstream of altered splice site) | 382 | 382 | BINDING | Substrate (By similarity). | might get lost (downstream of altered splice site) | 385 | 387 | STRAND | | might get lost (downstream of altered splice site) | 390 | 392 | HELIX | | might get lost (downstream of altered splice site) | 396 | 410 | HELIX | | might get lost (downstream of altered splice site) | 412 | 414 | TURN | | might get lost (downstream of altered splice site) | 419 | 429 | HELIX | | might get lost (downstream of altered splice site) | 430 | 430 | CONFLICT | H -> D (in Ref. 3; BAG52676). | might get lost (downstream of altered splice site) | 430 | 432 | TURN | | might get lost (downstream of altered splice site) | 439 | 441 | STRAND | | might get lost (downstream of altered splice site) | 442 | 442 | CONFLICT | Q -> P (in Ref. 2; AAL01037 and 7; AAC78841). | might get lost (downstream of altered splice site) | 442 | 447 | HELIX | | might get lost (downstream of altered splice site) | 450 | 453 | HELIX | | might get lost (downstream of altered splice site) | 458 | 461 | HELIX | | might get lost (downstream of altered splice site) | 465 | 468 | HELIX | | might get lost (downstream of altered splice site) | 488 | 491 | STRAND | | might get lost (downstream of altered splice site) | 496 | 502 | HELIX | | might get lost (downstream of altered splice site) | 561 | 561 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 589 | 589 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) |
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length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 1647 / 1647 |
position (AA) of stopcodon in wt / mu AA sequence | 549 / 549 |
position of stopcodon in wt / mu cDNA | 1966 / 1966 |
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 | 320 / 320 |
chromosome | 13 |
strand | -1 |
last intron/exon boundary | 1925 |
theoretical NMD boundary in CDS | 1555 |
length of CDS | 1647 |
coding sequence (CDS) position | 955 |
cDNA position (for ins/del: last normal base / first normal base) | 1274 |
gDNA position (for ins/del: last normal base / first normal base) | 30260 |
chromosomal position (for ins/del: last normal base / first normal base) | 25831888 |
original gDNA sequence snippet | AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGTAATA |
altered gDNA sequence snippet | AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGTAATA |
original cDNA sequence snippet | AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGCAATA |
altered cDNA sequence snippet | AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGCAATA |
wildtype AA sequence | MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS GLESSGWLRH IKAVMDAAIF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESLTSYS SFKIIVGQ* |
mutated AA sequence | MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS GLESSGWLRH IKAVMDAAVF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESLTSYS SFKIIVGQ* |
speed | 1.06 s |
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