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MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000220812
MT speed 0.04 s - this script 2.493009 s

Transcript summary:

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TranscriptGene symbolPredictionTree voteModelPrediction problemSplice site changeKnown ClinVar disease mutationPotential ClinVar disease mutationAmino acid changesVariant typedbSNP IDProtein lengthFeatures at a glance
ENST00000220812(MANE Select)
DKK4Deleterious82|17simple_aaeNoSingle base exchangeNormal
  • Amino acid sequence changed
  • Protein features (might be) affected
Yum, tasty mutations...

MutationT@ster 2025

Variant:

8:42375806C>A_1_ENST00000220812

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Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 82|17 (del | benign) ?
Analysed issue Analysis result
Variant Chr8:42375806C>A (GRCh38)
Gene symbol DKK4
Gene constraints LOEUF: 1.64, LOF (oe): 1.13, misssense (oe): 0.93, synonymous (oe): 0.80 ? (gnomAD)
Ensembl transcript ID ENST00000220812.3
Genbank transcript ID NM_014420 (exact from MANE)
UniProt / AlphaMissense peptide DKK4_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.136G>T
g.1424G>T
AA changes
AAE:D46Y?
Score:160
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs201742431
gnomADhomozygous (A/A)heterozygousallele carriers
02929
Protein conservation
SpeciesMatchGeneAAAlignment
Human      46ARKGSQCLSDTDCNTRKFCLQPRD
mutated  not conserved    46ARKGSQCLSDTYCNTRKFCLQPR
Ptroglodytes  all identical    46ARKGSQCLSDTDCNTRKFCLQPR
Mmulatta  all identical    46ARKGSQCLSDTDCNTRKFCLQSH
Fcatus  all identical    46ARKGSQCLSDKDCSSRKFCLKPQ
Mmusculus  all identical    46AGKGSLCASDRDCSEGKFCLAFH
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
Protein features
Start (aa)End (aa)FeatureDetails 
19224CHAINlost
4190REGIONlost
4446HELIXlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)6.8421
5.0311
(flanking)-1.4780
?
Splice sites No abrogation of potential splice sites predicted by MaxEntScan.
Distance from splice site 25
Kozak consensus sequence altered? No
poly(A) signal N/A
AA sequence altered Yes
Chromosome 8
Strand -1
Original gDNA sequence snippet CACAGTGCCTGTCTGACACGGACTGCAATACCAGAAAGTTC
Altered gDNA sequence snippet CACAGTGCCTGTCTGACACGTACTGCAATACCAGAAAGTTC
Original cDNA sequence snippet CACAGTGCCTGTCTGACACGGACTGCAATACCAGAAAGTTC
Altered cDNA sequence snippet CACAGTGCCTGTCTGACACGTACTGCAATACCAGAAAGTTC
Wildtype AA sequence MVAAVLLGLS WLCSPLGALV LDFNNIRSSA DLHGARKGSQ CLSDTDCNTR KFCLQPRDEK
PFCATCRGLR RRCQRDAMCC PGTLCVNDVC TTMEDATPIL ERQLDEQDGT HAEGTTGHPV
QENQPKRKPS IKKSQGRKGQ EGESCLRTFD CGPGLCCARH FWTKICKPVL LEGQVCSRRG
HKDTAQAPEI FQRCDCGPGL LCRSQLTSNR QHARLRVCQK IEKL*
Mutated AA sequence MVAAVLLGLS WLCSPLGALV LDFNNIRSSA DLHGARKGSQ CLSDTYCNTR KFCLQPRDEK
PFCATCRGLR RRCQRDAMCC PGTLCVNDVC TTMEDATPIL ERQLDEQDGT HAEGTTGHPV
QENQPKRKPS IKKSQGRKGQ EGESCLRTFD CGPGLCCARH FWTKICKPVL LEGQVCSRRG
HKDTAQAPEI FQRCDCGPGL LCRSQLTSNR QHARLRVCQK IEKL*
Position of stopcodon in wt / mu CDS 675 / 675
Position (AA) of stopcodon in wt / mu AA sequence 225 / 225
Position of stopcodon in wt / mu cDNA 859 / 859
Position of start ATG in wt / mu cDNA 185 / 185
Last intron/exon boundary 599
Theoretical NMD boundary in CDS 364
Length of CDS 675
Coding sequence (CDS) position 136
cDNA position 320
gDNA position 1424
Chromosomal position 42375806
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

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