Prediction |
polymorphism |
Model: simple_aae, prob: 0.859090968199527 (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) | chr11:102495998T>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | MMP20 |
| Ensembl transcript ID | ENST00000260228 |
| Genbank transcript ID | NM_004771 |
| UniProt peptide | O60882 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.53A>C
cDNA.66A>C
g.66A>C |
| AA changes | K18T Score: 78 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 18 |
| frameshift | no |
| known variant | Reference ID: rs2245803
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1152 | 1084 | 2236 |
| ExAC | 26807 | -20847 | 5960 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.362 | 0.972 | | 1.851 | 0.977 | | (flanking) | 1.129 | 0.965 |
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 | 75 | wt: 0.32 / mu: 0.76 | wt: CATGGCTTTGAAGTTTTCCACTGCAGCCCCCTCCCTAGTTG
mu: CATGGCTTTGACGTTTTCCACTGCAGCCCCCTCCCTAGTTG | ccac|TGCA | | Acc increased | 77 | wt: 0.32 / mu: 0.70 | wt: TGGCTTTGAAGTTTTCCACTGCAGCCCCCTCCCTAGTTGCA
mu: TGGCTTTGACGTTTTCCACTGCAGCCCCCTCCCTAGTTGCA | actg|CAGC | | Acc marginally increased | 56 | wt: 0.9388 / mu: 0.9531 (marginal change - not scored) | wt: GCCTTGCTGTCTTCCTCATCATGGCTTTGAAGTTTTCCACT
mu: GCCTTGCTGTCTTCCTCATCATGGCTTTGACGTTTTCCACT | atca|TGGC | | Acc marginally increased | 57 | wt: 0.9737 / mu: 0.9764 (marginal change - not scored) | wt: CCTTGCTGTCTTCCTCATCATGGCTTTGAAGTTTTCCACTG
mu: CCTTGCTGTCTTCCTCATCATGGCTTTGACGTTTTCCACTG | tcat|GGCT | | Acc gained | 63 | 0.32 | mu: TGTCTTCCTCATCATGGCTTTGACGTTTTCCACTGCAGCCC | cttt|GACG | | Acc gained | 73 | 0.45 | mu: ATCATGGCTTTGACGTTTTCCACTGCAGCCCCCTCCCTAGT | ttcc|ACTG |
|
| distance from splice site | 66 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 18 | S | G | L | A | V | F | L | I | M | A | L | K | F | S | T | A | A | P | S | L | V | A | A | S |
| mutated | not conserved | | 18 | S | G | L | A | V | F | L | I | M | A | L | T | F | S | T | A | A | P | S | L | V | A | A |
| Ptroglodytes | all identical | ENSPTRG00000004216 | 18 | S | G | L | A | V | F | L | I | M | A | L | K | F | S | T | A | A | P | S | L | V | A | A |
| Mmulatta | all identical | ENSMMUG00000011013 | 18 | S | G | L | A | V | L | L | I | M | A | L | K | F | S | T | A | A | P | S | L | V | A | A |
| Fcatus | all identical | ENSFCAG00000015788 | 18 | S | G | L | A | V | L | L | V | T | A | L | K | F | S | T | A | A | P | S | P | P | A | A |
| Mmusculus | all identical | ENSMUSG00000018620 | 18 | S | G | L | A | V | - | L | V | T | A | L | K | F | A | T | A | D | P | N | L | L | A | A |
| Ggallus | no homologue | | | |
| Trubripes | not conserved | ENSTRUG00000005045 | 15 | | | | | | | V | L | L | S | C | V | F | L | T | D | A | A | P | T | I | A | P |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000034187 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 22 | SIGNAL | Potential. | lost | | 23 | 107 | PROPEP | By similarity. /FTId=PRO_0000028833. | might get lost (downstream of altered splice site) | | 98 | 105 | MOTIF | Cysteine switch (By similarity). | might get lost (downstream of altered splice site) | | 100 | 100 | METAL | Zinc; in inhibited form (By similarity). | might get lost (downstream of altered splice site) | | 120 | 126 | STRAND | | might get lost (downstream of altered splice site) | | 131 | 133 | STRAND | | might get lost (downstream of altered splice site) | | 135 | 152 | HELIX | | might get lost (downstream of altered splice site) | | 156 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 161 | 163 | STRAND | | might get lost (downstream of altered splice site) | | 166 | 172 | STRAND | | might get lost (downstream of altered splice site) | | 176 | 180 | STRAND | | might get lost (downstream of altered splice site) | | 184 | 187 | STRAND | | might get lost (downstream of altered splice site) | | 189 | 192 | STRAND | | might get lost (downstream of altered splice site) | | 195 | 199 | STRAND | | might get lost (downstream of altered splice site) | | 203 | 206 | STRAND | | might get lost (downstream of altered splice site) | | 208 | 208 | CONFLICT | A -> P (in Ref. 1; CAA73317). | might get lost (downstream of altered splice site) | | 211 | 219 | STRAND | | might get lost (downstream of altered splice site) | | 220 | 232 | HELIX | | might get lost (downstream of altered splice site) | | 226 | 226 | METAL | Zinc; catalytic (By similarity). | might get lost (downstream of altered splice site) | | 227 | 227 | ACT_SITE | By similarity. | might get lost (downstream of altered splice site) | | 230 | 230 | METAL | Zinc; catalytic (By similarity). | might get lost (downstream of altered splice site) | | 236 | 236 | METAL | Zinc; catalytic (By similarity). | might get lost (downstream of altered splice site) | | 253 | 255 | TURN | | might get lost (downstream of altered splice site) | | 261 | 270 | HELIX | | might get lost (downstream of altered splice site) | | 296 | 296 | DISULFID | Potential. | might get lost (downstream of altered splice site) | | 302 | 345 | DOMAIN | Hemopexin-like 1. | might get lost (downstream of altered splice site) | | 347 | 389 | DOMAIN | Hemopexin-like 2. | might get lost (downstream of altered splice site) | | 394 | 441 | DOMAIN | Hemopexin-like 3. | might get lost (downstream of altered splice site) | | 443 | 483 | DOMAIN | Hemopexin-like 4. | might get lost (downstream of altered splice site) | | 483 | 483 | DISULFID | Potential. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1452 / 1452 |
| position (AA) of stopcodon in wt / mu AA sequence | 484 / 484 |
| position of stopcodon in wt / mu cDNA | 1465 / 1465 |
| 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 | 14 / 14 |
| chromosome | 11 |
| strand | -1 |
| last intron/exon boundary | 1365 |
| theoretical NMD boundary in CDS | 1301 |
| length of CDS | 1452 |
| coding sequence (CDS) position | 53 |
cDNA position
(for ins/del: last normal base / first normal base) | 66 |
gDNA position
(for ins/del: last normal base / first normal base) | 66 |
chromosomal position
(for ins/del: last normal base / first normal base) | 102495998 |
| original gDNA sequence snippet | CTTCCTCATCATGGCTTTGAAGTTTTCCACTGCAGCCCCCT |
| altered gDNA sequence snippet | CTTCCTCATCATGGCTTTGACGTTTTCCACTGCAGCCCCCT |
| original cDNA sequence snippet | CTTCCTCATCATGGCTTTGAAGTTTTCCACTGCAGCCCCCT |
| altered cDNA sequence snippet | CTTCCTCATCATGGCTTTGACGTTTTCCACTGCAGCCCCCT |
| wildtype AA sequence | MKVLPASGLA VFLIMALKFS TAAPSLVAAS PRTWRNNYRL AQAYLDKYYT NKEGHQIGEM
VARGSNSMIR KIKELQAFFG LQVTGKLDQT TMNVIKKPRC GVPDVANYRL FPGEPKWKKN
TLTYRISKYT PSMSSVEVDK AVEMALQAWS SAVPLSFVRI NSGEADIMIS FENGDHGDSY
PFDGPRGTLA HAFAPGEGLG GDTHFDNAEK WTMGTNGFNL FTVAAHEFGH ALGLAHSTDP
SALMYPTYKY KNPYGFHLPK DDVKGIQALY GPRKVFLGKP TLPHAPHHKP SIPDLCDSSS
SFDAVTMLGK ELLLFKDRIF WRRQVHLRTG IRPSTITSSF PQLMSNVDAA YEVAERGTAY
FFKGPHYWIT RGFQMQGPPR TIYDFGFPRH VQQIDAAVYL REPQKTLFFV GDEYYSYDER
KRKMEKDYPK NTEEEFSGVN GQIDAAVELN GYIYFFSGPK TYKYDTEKED VVSVVKSSSW
IGC* |
| mutated AA sequence | MKVLPASGLA VFLIMALTFS TAAPSLVAAS PRTWRNNYRL AQAYLDKYYT NKEGHQIGEM
VARGSNSMIR KIKELQAFFG LQVTGKLDQT TMNVIKKPRC GVPDVANYRL FPGEPKWKKN
TLTYRISKYT PSMSSVEVDK AVEMALQAWS SAVPLSFVRI NSGEADIMIS FENGDHGDSY
PFDGPRGTLA HAFAPGEGLG GDTHFDNAEK WTMGTNGFNL FTVAAHEFGH ALGLAHSTDP
SALMYPTYKY KNPYGFHLPK DDVKGIQALY GPRKVFLGKP TLPHAPHHKP SIPDLCDSSS
SFDAVTMLGK ELLLFKDRIF WRRQVHLRTG IRPSTITSSF PQLMSNVDAA YEVAERGTAY
FFKGPHYWIT RGFQMQGPPR TIYDFGFPRH VQQIDAAVYL REPQKTLFFV GDEYYSYDER
KRKMEKDYPK NTEEEFSGVN GQIDAAVELN GYIYFFSGPK TYKYDTEKED VVSVVKSSSW
IGC* |
| speed | 0.11 s |
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