| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000337331(MANE Select) | NPHP3 | Benign | 1|99 | 3utr | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:132681253G>A (GRCh38) | |||||||||||||
| Gene symbol | NPHP3 | |||||||||||||
| Gene constraints | LOEUF: 0.87, LOF (oe): 0.73, misssense (oe): 0.93, synonymous (oe): 0.95 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000337331.10 | |||||||||||||
| Genbank transcript ID | NM_153240 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 3'UTR | |||||||||||||
| DNA changes | cDNA.4704C>T g.41180C>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | polyA signal ok | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | AAAAAAAAAAAAAAAGAATTCCATGATTCTTTTGAGCTCTC | |||||||||||||
| Altered gDNA sequence snippet | AAAAAAAAAAAAAAAGAATTTCATGATTCTTTTGAGCTCTC | |||||||||||||
| Original cDNA sequence snippet | AAAAAAAAAAAAAAAGAATTCCATGATTCTTTTGAGCTCTC | |||||||||||||
| Altered cDNA sequence snippet | AAAAAAAAAAAAAAAGAATTTCATGATTCTTTTGAGCTCTC | |||||||||||||
| Wildtype AA sequence | MGTASSLVSP AGGEVIEDTY GAGGGEACEI PVEVKPKARL LRNSFRRGAG AAAGAGPGSL PRGVGAGGLL GASFKSTGSS VPELEYAAAE YERLRKEYEI FRVSKNQELL SMGRREAKLD TENKRLRAEL QALQKTYQKI LREKESALEA KYQAMERAAT FEHDRDKVKR QFKIFRETKE NEIQDLLRAK RELESKLQRL QAQGIQVFDP GESDSDDNCT DVTAAGTQCE YWTGGALGSE PSIGSMIQLQ QSFRGPEFAH SSIDVEGPFA NVNRDDWDIA VASLLQVTPL FSHSLWSNTV RCYLIYTDET QPEMDLFLKD YSPKLKRMCE TMGYFFHAVY FPIDVENQYL TVRKWEIEKS SLVILFIHLT LPSLLLEDCE EAFLKNPEGK PRLIFHRLED GKVSSDSVQQ LIDQVSNLNK TSKAKIIDHS GDPAEGVYKT YICVEKIIKQ DILGFENTDL ETKDLGSEDS IPEEDDFGDV LWDIHDEQEQ METFQQASNS AHELGFEKYY QRLNDLVAAP APIPPLLVSG GPGSGKSLLL SKWIQLQQKN SPNTLILSHF VGRPMSTSSE SSLIIKRLTL KLMQHSWSVS ALTLDPAKLL EEFPRWLEKL SARHQGSIII VIDSIDQVQQ VEKHMKWLID PLPVNVRVIV SVNVETCPPA WRLWPTLHLD PLSPKDAKSI IIAECHSVDI KLSKEQEKKL ERHCRSATTC NALYVTLFGK MIARAGRAGN LDKILHQCFQ CQDTLSLYRL VLHSIRESMA NDVDKELMKQ ILCLVNVSHN GVSESELMEL YPEMSWTFLT SLIHSLYKMC LLTYGCGLLR FQHLQAWETV RLEYLEGPTV TSSYRQKLIN YFTLQLSQDR VTWRSADELP WLFQQQGSKQ KLHDCLLNLF VSQNLYKRGH FAELLSYWQF VGKDKSAMAT EYFDSLKQYE KNCEGEDNMS CLADLYETLG RFLKDLGLLS QAIVPLQRSL EIRETALDPD HPRVAQSLHQ LASVYVQWKK FGNAEQLYKQ ALEISENAYG ADHPYTAREL EALATLYQKQ NKYEQAEHFR KKSFKIHQKA IKKKGNLYGF ALLRRRALQL EELTLGKDTP DNARTLNELG VLYYLQNNLE TADQFLKRSL EMRERVLGPD HPDCAQSLNN LAALCNEKKQ YDKAEELYER ALDIRRRALA PDHPSLAYTV KHLAILYKKM GKLDKAVPLY ELAVEIRQKS FGPKHPSVAT ALVNLAVLYS QMKKHVEALP LYERALKIYE DSLGRMHPRV GETLKNLAVL SYEGGDFEKA AELYKRAMEI KEAETSLLGG KAPSRHSSSG DTFSLKTAHS PNVFLQQGQR * | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| 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 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 55 / 55 | |||||||||||||
| Last intron/exon boundary | 3866 | |||||||||||||
| Theoretical NMD boundary in CDS | 3761 | |||||||||||||
| Length of CDS | 3993 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 4704 | |||||||||||||
| gDNA position | 41180 | |||||||||||||
| Chromosomal position | 132681253 | |||||||||||||
| Speed | 0.04 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project