Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999967550892 (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) | chr20:43933021G>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | MATN4 |
| Ensembl transcript ID | ENST00000342716 |
| Genbank transcript ID | NM_003833 |
| UniProt peptide | O95460 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.490C>A
cDNA.677C>A
g.4149C>A |
| AA changes | R164S Score: 110 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 164 |
| frameshift | no |
| known variant | Reference ID: rs2072788
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | 494 | 994 | 1488 |
| ExAC | 6683 | 19401 | 26084 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.254 | 0.146 | | 0.687 | 0.162 | | (flanking) | -0.004 | 0.177 |
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 | | Donor gained | 4149 | 0.31 | mu: GCGCCAGCGGCATTG | GCCA|gcgg |
|
| distance from splice site | 154 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 164 | R | V | A | E | V | A | A | Q | A | R | A | R | G | I | E | I | Y | A | V | G | V | Q | R | A |
| mutated | not conserved | | 164 | R | V | A | E | V | A | A | Q | A | R | A | S | G | I | E | I | Y | A | V | G | V | Q | R |
| Ptroglodytes | all identical | ENSPTRG00000013541 | 164 | R | V | A | E | V | A | A | Q | A | R | A | R | G | I | E | I | Y | A | V | G | V | Q | R |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | all identical | ENSMUSG00000016995 | 166 | R | V | A | E | V | A | A | Q | A | R | A | R | G | I | E | I | Y | A | V | G | V | Q | R |
| Ggallus | not conserved | ENSGALG00000004028 | 164 | R | V | S | E | V | A | A | H | A | R | N | A | G | I | E | I | Y | A | V | G | I | Q | R |
| Trubripes | all conserved | ENSTRUG00000000492 | 81 | R | V | A | E | V | A | A | E | A | R | G | K | G | I | E | I | Y | A | V | G | V | A | R |
| Drerio | not conserved | ENSDARG00000015947 | 165 | R | V | A | E | V | A | A | A | A | R | E | S | G | I | E | I | Y | A | V | G | V | A | R |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 34 | 213 | DOMAIN | VWFA 1. | lost | | 173 | 173 | CONFLICT | V -> L (in Ref. 2; BAC11083). | might get lost (downstream of altered splice site) | | 215 | 255 | DOMAIN | EGF-like 1; incomplete. | might get lost (downstream of altered splice site) | | 219 | 219 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 226 | 226 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 230 | 230 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 239 | 239 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 241 | 241 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 251 | 251 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 254 | 254 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 256 | 292 | DOMAIN | EGF-like 2. | might get lost (downstream of altered splice site) | | 260 | 260 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 267 | 267 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 271 | 271 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 280 | 280 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 282 | 282 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 295 | 295 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 297 | 337 | DOMAIN | EGF-like 3. | might get lost (downstream of altered splice site) | | 301 | 301 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 305 | 305 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 308 | 308 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 312 | 312 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 321 | 321 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 323 | 323 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 336 | 336 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 342 | 342 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 342 | 377 | DOMAIN | EGF-like 4. | might get lost (downstream of altered splice site) | | 349 | 349 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 353 | 353 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 362 | 362 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 364 | 364 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 377 | 377 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 386 | 561 | DOMAIN | VWFA 2. | might get lost (downstream of altered splice site) | | 563 | 563 | CONFLICT | G -> S (in Ref. 2; BAC11083). | might get lost (downstream of altered splice site) | | 591 | 622 | COILED | Potential. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1746 / 1746 |
| position (AA) of stopcodon in wt / mu AA sequence | 582 / 582 |
| position of stopcodon in wt / mu cDNA | 1933 / 1933 |
| 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 | 188 / 188 |
| chromosome | 20 |
| strand | -1 |
| last intron/exon boundary | 1875 |
| theoretical NMD boundary in CDS | 1637 |
| length of CDS | 1746 |
| coding sequence (CDS) position | 490 |
cDNA position
(for ins/del: last normal base / first normal base) | 677 |
gDNA position
(for ins/del: last normal base / first normal base) | 4149 |
chromosomal position
(for ins/del: last normal base / first normal base) | 43933021 |
| original gDNA sequence snippet | TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG |
| altered gDNA sequence snippet | TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG |
| original cDNA sequence snippet | TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG |
| altered cDNA sequence snippet | TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG |
| wildtype AA sequence | MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARARGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K* |
| mutated AA sequence | MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K* |
| speed | 1.04 s |
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