1-1435798-TGGCGCGGAGC-TGGCGCGGAGCGGCGCGGAGC
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_022834.5(VWA1):c.62_71dupGCGCGGAGCG(p.Gly25ArgfsTer74) variant causes a frameshift, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000931 in 1,202,546 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_022834.5 frameshift, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWA1 | NM_022834.5 | c.62_71dupGCGCGGAGCG | p.Gly25ArgfsTer74 | frameshift_variant, splice_region_variant | Exon 1 of 3 | ENST00000476993.2 | NP_073745.2 | |
VWA1 | NM_199121.3 | c.62_71dupGCGCGGAGCG | p.Gly25ArgfsTer53 | frameshift_variant, splice_region_variant | Exon 1 of 3 | NP_954572.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWA1 | ENST00000476993.2 | c.62_71dupGCGCGGAGCG | p.Gly25ArgfsTer74 | frameshift_variant, splice_region_variant | Exon 1 of 3 | 1 | NM_022834.5 | ENSP00000417185.1 | ||
VWA1 | ENST00000471398.1 | c.62_71dupGCGCGGAGCG | p.Gly25ArgfsTer14 | frameshift_variant, splice_region_variant | Exon 1 of 2 | 3 | ENSP00000464343.1 | |||
VWA1 | ENST00000338660.5 | c.62_71dupGCGCGGAGCG | p.Gly25ArgfsTer53 | frameshift_variant, splice_region_variant | Exon 1 of 3 | 2 | ENSP00000423404.1 | |||
VWA1 | ENST00000495558.1 | c.-33+664_-33+673dupGCGCGGAGCG | intron_variant | Intron 1 of 1 | 2 | ENSP00000463643.1 |
Frequencies
GnomAD3 genomes AF: 0.000669 AC: 100AN: 149504Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000969 AC: 1020AN: 1052936Hom.: 1 Cov.: 31 AF XY: 0.000991 AC XY: 507AN XY: 511496
GnomAD4 genome AF: 0.000668 AC: 100AN: 149610Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 47AN XY: 73002
ClinVar
Submissions by phenotype
Neuronopathy, distal hereditary motor, autosomal recessive 7 Pathogenic:5
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This frameshifting variant in exon 1 of 3 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported as a compound heterozygous or homozygous change in individuals with neuromyopathy (PMID: 33459760) and hereditary motor neuropathy (PMID: 33559681). The c.62_71dup (p.Gly25ArgfsTer74) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.0333% (15/45050) and thus is presumed to be rare. Based on the available evidence, the c.62_71dup (p.Gly25ArgfsTer74) variant is classified as Pathogenic. -
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Sequencing funded by the International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD): https://www.ucl.ac.uk/genomic-medicine-neuromuscular-diseases/. -
not provided Pathogenic:2
VWA1: PVS1, PM2, PM3 -
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Neuromuscular disease Pathogenic:1
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VWA1-related disorder Pathogenic:1
The VWA1 c.62_71dup10 variant is predicted to result in a frameshift and premature protein termination (p.Gly25Argfs*74). This variant has been reported in the compound heterozygous and homozygous state in individuals from mutliple unrelated families with neuromyopathy (Deschauer et al 2021. PubMed ID: 33459760; Pagnamenta AT et al 2021. PubMed ID: 33559681). This variant is reported in 0.070% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-1371178-T-TGGCGCGGAGC). Frameshift variants in VWA1 are expected to be pathogenic. This variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at