Prediction |
disease causing |
Model: simple_aae, prob: 0.999999997493906 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM031989)
- known disease mutation at this position (HGMD CM1514360)
- known disease mutation: rs16249 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr2:49190614G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | FSHR |
| Ensembl transcript ID | ENST00000346173 |
| Genbank transcript ID | N/A |
| UniProt peptide | P23945 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.1160C>T
cDNA.1270C>T
g.191063C>T |
| AA changes | T387I Score: 89 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 387 |
| frameshift | no |
| known variant | Reference ID: rs28928870
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16249 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1514360)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031989)
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -1.992 | 0.076 | | 5.977 | 1 | | (flanking) | 2.296 | 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 | 191069 | wt: 0.73 / mu: 0.82 | wt: TGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCT
mu: TGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCT | tctt|TGCC | | Acc marginally increased | 191070 | wt: 0.8597 / mu: 0.8632 (marginal change - not scored) | wt: GCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTA
mu: GCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTA | cttt|GCCA | | Acc increased | 191062 | wt: 0.39 / mu: 0.45 | wt: GTGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTG
mu: GTGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTG | ttca|CTGT | | Acc marginally increased | 191071 | wt: 0.8714 / mu: 0.9260 (marginal change - not scored) | wt: CTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTAC
mu: CTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTAC | tttg|CCAG | | Acc marginally increased | 191072 | wt: 0.9318 / mu: 0.9611 (marginal change - not scored) | wt: TGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTACA
mu: TGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTACA | ttgc|CAGT | | Acc marginally increased | 191068 | wt: 0.9908 / mu: 0.9944 (marginal change - not scored) | wt: CTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTC
mu: CTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTC | gtct|TTGC | | Acc increased | 191065 | wt: 0.63 / mu: 0.78 | wt: ATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCA
mu: ATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCA | actg|TCTT | | Acc marginally increased | 191074 | wt: 0.9925 / mu: 0.9948 (marginal change - not scored) | wt: GCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAGTCTACACT
mu: GCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAGTCTACACT | gcca|GTGA | | Acc marginally increased | 191061 | wt: 0.8817 / mu: 0.9376 (marginal change - not scored) | wt: TGTGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCT
mu: TGTGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCT | tttc|ACTG | | Acc marginally increased | 191066 | wt: 0.7906 / mu: 0.8393 (marginal change - not scored) | wt: TGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGTCAG
mu: TGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGTCAG | ctgt|CTTT |
|
| distance from splice site | 492 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 387 | T | G | A | G | C | D | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L | T |
| mutated | not conserved | | 387 | T | G | A | G | C | D | A | A | G | F | F | I | V | F | A | S | E | L | S | V | Y | T | L |
| Ptroglodytes | all identical | ENSPTRG00000011914 | 449 | T | G | A | G | C | D | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L |
| Mmulatta | all identical | ENSMMUG00000017196 | 449 | T | G | A | G | C | D | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L |
| Fcatus | all identical | ENSFCAG00000001215 | 449 | T | G | A | G | C | D | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L |
| Mmusculus | all identical | ENSMUSG00000032937 | 448 | T | G | A | G | C | D | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L |
| Ggallus | all identical | ENSGALG00000009100 | 449 | T | G | A | G | C | N | A | A | G | F | F | T | V | F | A | S | E | L | S | V | Y | T | L |
| Trubripes | no homologue | | | |
| Drerio | all identical | ENSDARG00000071494 | 430 | T | G | A | G | C | H | V | A | G | F | F | T | V | F | S | S | E | L | S | V | Y | T | L |
| Dmelanogaster | all identical | FBgn0016650 | 576 | | | | | | K | V | A | G | F | L | T | V | F | A | S | H | L | S | V | F | T | L |
| Celegans | not conserved | C50H2.1 | 517 | T | G | W | G | C | R | A | A | G | F | L | A | V | F | A | S | E | L | G | I | I | S | M |
| Xtropicalis | all identical | ENSXETG00000025827 | 351 | T | G | A | G | C | H | A | A | G | F | F | T | V | F | A | S | E | L | S | V | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 367 | 387 | TRANSMEM | Helical; Name=1; (Potential). | lost | | 388 | 398 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 399 | 421 | TRANSMEM | Helical; Name=2; (Potential). | might get lost (downstream of altered splice site) | | 422 | 443 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 442 | 442 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 444 | 465 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | | 466 | 485 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 486 | 508 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | | 509 | 528 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 517 | 517 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 529 | 550 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | | 551 | 573 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 574 | 597 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | | 598 | 608 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 609 | 630 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 631 | 695 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1902 / 1902 |
| position (AA) of stopcodon in wt / mu AA sequence | 634 / 634 |
| position of stopcodon in wt / mu cDNA | 2012 / 2012 |
| 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 | 111 / 111 |
| chromosome | 2 |
| strand | -1 |
| last intron/exon boundary | 779 |
| theoretical NMD boundary in CDS | 618 |
| length of CDS | 1902 |
| coding sequence (CDS) position | 1160 |
cDNA position
(for ins/del: last normal base / first normal base) | 1270 |
gDNA position
(for ins/del: last normal base / first normal base) | 191063 |
chromosomal position
(for ins/del: last normal base / first normal base) | 49190614 |
| original gDNA sequence snippet | TGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGT |
| altered gDNA sequence snippet | TGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGT |
| original cDNA sequence snippet | TGATGCTGCTGGCTTTTTCACTGTCTTTGCCAGTGAGCTGT |
| altered cDNA sequence snippet | TGATGCTGCTGGCTTTTTCATTGTCTTTGCCAGTGAGCTGT |
| wildtype AA sequence | MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFTVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN* |
| mutated AA sequence | MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFIVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN* |
| speed | 0.55 s |
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