Yum, tasty mutations...

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: ENST00000361866
MT speed 0.06 s - this script 2.511254 s

Transcript summary:

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Yum, tasty mutations...

MutationT@ster 2025

Variant:

21:46003540C>T_1_ENST00000361866

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Prediction:

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Summary:

  • Model: simple_aae
  • Tree vote: 72|28 (del | benign) ?
Analysed issue Analysis result
Variant Chr21:46003540C>T (GRCh38)
Gene symbol COL6A1
Gene constraints LOEUF: 0.71, LOF (oe): 0.58, misssense (oe): 0.97, synonymous (oe): 1.05 ? (gnomAD)
Ensembl transcript ID ENST00000361866.8
Genbank transcript ID NM_001848 (exact from MANE)
UniProt / AlphaMissense peptide CO6A1_HUMAN | AlphaMissense: transcript, gene
Variant type Single base exchange
Gene region CDS
DNA changes c.2614C>T
g.21771C>T
AA changes
AAE:R872W?
Score:101
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs368561027
gnomADhomozygous (T/T)heterozygousallele carriers
08080
Protein conservation
SpeciesMatchGeneAAAlignment
Human      872TAGRTDPAHDVRVAVVQYSGTGQQ
mutated  not conserved    872TAGRTDPAHDVWVAVVQYSGTGQ
Ptroglodytes  no homologue    
Mmulatta  all identical    872MAGRTDPAHDVRVAVVQYSGTGQ
Fcatus  all identical    871TAGKTNPSHDVRVSVVQYSGPGQ
Mmusculus  all identical    869SAGRADPSQDVRVAVVQYSGQGQ
Ggallus  all identical    998VRVSVVQYSGRNQ
Trubripes  all identical    732TADRQGSAL-VRVGVGQYS----
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
Protein features
Start (aa)End (aa)FeatureDetails 
201028CHAINlost
5931028REGIONC-terminallost
8291021DOMAINVWFAlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)0.3860.998
3.4261
(flanking)3.0840.998
?
Splice sites No abrogation of potential splice sites predicted by MaxEntScan.
Distance from splice site N/A
Kozak consensus sequence altered? No
poly(A) signal N/A
AA sequence altered Yes
Chromosome 21
Strand 1
Original gDNA sequence snippet CGGACCCCGCCCACGACGTGCGGGTGGCGGTGGTGCAGTAC
Altered gDNA sequence snippet CGGACCCCGCCCACGACGTGTGGGTGGCGGTGGTGCAGTAC
Original cDNA sequence snippet CGGACCCCGCCCACGACGTGCGGGTGGCGGTGGTGCAGTAC
Altered cDNA sequence snippet CGGACCCCGCCCACGACGTGTGGGTGGCGGTGGTGCAGTAC
Wildtype AA sequence MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD
KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV
KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG GLEDAVNEAK
HLGVKVFSVA ITPDHLEPRL SIIATDHTYR RNFTAADWGQ SRDAEEAISQ TIDTIVDMIK
NNVEQVCCSF ECQPARGPPG LRGDPGFEGE RGKPGLPGEK GEAGDPGRPG DLGPVGYQGM
KGEKGSRGEK GSRGPKGYKG EKGKRGIDGV DGVKGEMGYP GLPGCKGSPG FDGIQGPPGP
KGDPGAFGLK GEKGEPGADG EAGRPGSSGP SGDEGQPGEP GPPGEKGEAG DEGNPGPDGA
PGERGGPGER GPRGTPGTRG PRGDPGEAGP QGDQGREGPV GVPGDPGEAG PIGPKGYRGD
EGPPGSEGAR GAPGPAGPPG DPGLMGERGE DGPAGNGTEG FPGFPGYPGN RGAPGINGTK
GYPGLKGDEG EAGDPGDDNN DIAPRGVKGA KGYRGPEGPQ GPPGHQGPPG PDECEILDII
MKMCSCCECK CGPIDLLFVL DSSESIGLQN FEIAKDFVVK VIDRLSRDEL VKFEPGQSYA
GVVQYSHSQM QEHVSLRSPS IRNVQELKEA IKSLQWMAGG TFTGEALQYT RDQLLPPSPN
NRIALVITDG RSDTQRDTTP LNVLCSPGIQ VVSVGIKDVF DFIPGSDQLN VISCQGLAPS
QGRPGLSLVK ENYAELLEDA FLKNVTAQIC IDKKCPDYTC PITFSSPADI TILLDGSASV
GSHNFDTTKR FAKRLAERFL TAGRTDPAHD VRVAVVQYSG TGQQRPERAS LQFLQNYTAL
ASAVDAMDFI NDATDVNDAL GYVTRFYREA SSGAAKKRLL LFSDGNSQGA TPAAIEKAVQ
EAQRAGIEIF VVVVGRQVNE PHIRVLVTGK TAEYDVAYGE SHLFRVPSYQ ALLRGVFHQT
VSRKVALG*
Mutated AA sequence MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD
KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV
KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG GLEDAVNEAK
HLGVKVFSVA ITPDHLEPRL SIIATDHTYR RNFTAADWGQ SRDAEEAISQ TIDTIVDMIK
NNVEQVCCSF ECQPARGPPG LRGDPGFEGE RGKPGLPGEK GEAGDPGRPG DLGPVGYQGM
KGEKGSRGEK GSRGPKGYKG EKGKRGIDGV DGVKGEMGYP GLPGCKGSPG FDGIQGPPGP
KGDPGAFGLK GEKGEPGADG EAGRPGSSGP SGDEGQPGEP GPPGEKGEAG DEGNPGPDGA
PGERGGPGER GPRGTPGTRG PRGDPGEAGP QGDQGREGPV GVPGDPGEAG PIGPKGYRGD
EGPPGSEGAR GAPGPAGPPG DPGLMGERGE DGPAGNGTEG FPGFPGYPGN RGAPGINGTK
GYPGLKGDEG EAGDPGDDNN DIAPRGVKGA KGYRGPEGPQ GPPGHQGPPG PDECEILDII
MKMCSCCECK CGPIDLLFVL DSSESIGLQN FEIAKDFVVK VIDRLSRDEL VKFEPGQSYA
GVVQYSHSQM QEHVSLRSPS IRNVQELKEA IKSLQWMAGG TFTGEALQYT RDQLLPPSPN
NRIALVITDG RSDTQRDTTP LNVLCSPGIQ VVSVGIKDVF DFIPGSDQLN VISCQGLAPS
QGRPGLSLVK ENYAELLEDA FLKNVTAQIC IDKKCPDYTC PITFSSPADI TILLDGSASV
GSHNFDTTKR FAKRLAERFL TAGRTDPAHD VWVAVVQYSG TGQQRPERAS LQFLQNYTAL
ASAVDAMDFI NDATDVNDAL GYVTRFYREA SSGAAKKRLL LFSDGNSQGA TPAAIEKAVQ
EAQRAGIEIF VVVVGRQVNE PHIRVLVTGK TAEYDVAYGE SHLFRVPSYQ ALLRGVFHQT
VSRKVALG*
Position of stopcodon in wt / mu CDS 3087 / 3087
Position (AA) of stopcodon in wt / mu AA sequence 1029 / 1029
Position of stopcodon in wt / mu cDNA 3168 / 3168
Position of start ATG in wt / mu cDNA 82 / 82
Last intron/exon boundary 2545
Theoretical NMD boundary in CDS 2413
Length of CDS 3087
Coding sequence (CDS) position 2614
cDNA position 2695
gDNA position 21771
Chromosomal position 46003540
Speed 0.06 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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