5-83536654-TCTTAATTTTACTCTTTTTGCAGTTCACACAAAGATGAATTCCTGCACTTCAAGATTACATTGTATATGTGATTCCTTGCTTCATTTTAAGGACTATGTTGTTTTCTTAAATGTGTTGATGAGTCTTTATAACCTGTTTTAATAATGTTAAATTGAATTCATTTTTCTTATTGTTAATACAAAAACAGTAAATTTGAAGACTGAGAACCATATAAGAGGGTGATTGCACTTATTATGAAAAGATTTGAATCCTTCTTTGTGTGTGTGGGTGTGACCAGCCTTGCTATCAATTTCTTCTGTCATACACTGCCAAATTTTCTATTTAAGTATTGTGAAAACTCTGTTTTTTTCAGGTCGAATGAGTGATTTGAGTGTAATTGGTCATCCAATAGATTCAGAATCTAAAGAAGATGAACCTTGTAGTGAAGAAACAGATCCAGTGCATGATCTAATGGCTGAAATTTTACCTGAATTCCCTGACATAATTGAAATAGACCTATACCACAGTGAAGAAAATGAAGAAGAAGAAGAAGAGTGTGCAAATGCTACTGATGTGACAACCACCCCATCTGTGCAGTACATAAATGGGAAGCATCTCGTTACCACTGTGCCCAAGGACCCAGAAGCTGCAGAAGCTAGGCGTGGCCAGTTTGAAAGTGTTGCACCTTCTCAGAATTTCTCGGACAGCTCTGAAAGTGATACTCATCCATTTGTAATAGCCAAAACGGAATTGTCTACTGCTGTGCAACCTAATGAATCTACAGAAACAACTGAGTCTCTTGAAGTTACATGGAAGCCTGAGACTTACC-T
- chr5-83536654-TCTTAATTTTACTCTTTTTGCAGTTCACACAAAGATGAATTCCTGCACTTCAAGATTACATTGTATATGTGATTCCTTGCTTCATTTTAAGGACTATGTTGTTTTCTTAAATGTGTTGATGAGTCTTTATAACCTGTTTTAATAATGTTAAATTGAATTCATTTTTCTTATTGTTAATACAAAAACAGTAAATTTGAAGACTGAGAACCATATAAGAGGGTGATTGCACTTATTATGAAAAGATTTGAATCCTTCTTTGTGTGTGTGGGTGTGACCAGCCTTGCTATCAATTTCTTCTGTCATACACTGCCAAATTTTCTATTTAAGTATTGTGAAAACTCTGTTTTTTTCAGGTCGAATGAGTGATTTGAGTGTAATTGGTCATCCAATAGATTCAGAATCTAAAGAAGATGAACCTTGTAGTGAAGAAACAGATCCAGTGCATGATCTAATGGCTGAAATTTTACCTGAATTCCCTGACATAATTGAAATAGACCTATACCACAGTGAAGAAAATGAAGAAGAAGAAGAAGAGTGTGCAAATGCTACTGATGTGACAACCACCCCATCTGTGCAGTACATAAATGGGAAGCATCTCGTTACCACTGTGCCCAAGGACCCAGAAGCTGCAGAAGCTAGGCGTGGCCAGTTTGAAAGTGTTGCACCTTCTCAGAATTTCTCGGACAGCTCTGAAAGTGATACTCATCCATTTGTAATAGCCAAAACGGAATTGTCTACTGCTGTGCAACCTAATGAATCTACAGAAACAACTGAGTCTCTTGAAGTTACATGGAAGCCTGAGACTTACC-T
- NM_004385.5:c.4004-350_4461del
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_004385.5(VCAN):c.4004-350_4461del(p.Arg1336fs) variant causes a frameshift, splice acceptor, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004385.5 frameshift, splice_acceptor, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.4004-350_4461del | p.Arg1336fs | frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant | Exon 8 of 15 | ENST00000265077.8 | NP_004376.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This variant is not present in population databases (gnomAD no frequency). This variant results in the deletion of part of exon 8 (c.4004-350_4461del) of the VCAN gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VCAN are known to be pathogenic (PMID: 26720455). This variant has not been reported in the literature in individuals affected with VCAN-related conditions. ClinVar contains an entry for this variant (Variation ID: 2024338). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.