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

Genomes: 𝑓 0.00067 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00097 ( 1 hom. )

Consequence

VWA1
NM_022834.5 frameshift, splice_region

Scores

Not classified

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: 0.706
Variant links:
Genes affected
VWA1 (HGNC:30910): (von Willebrand factor A domain containing 1) VWA1 belongs to the von Willebrand factor (VWF; MIM 613160) A (VWFA) domain superfamily of extracellular matrix proteins and appears to play a role in cartilage structure and function (Fitzgerald et al., 2002 [PubMed 12062410]).[supplied by OMIM, Nov 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 11 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-1435798-T-TGGCGCGGAGC is Pathogenic according to our data. Variant chr1-1435798-T-TGGCGCGGAGC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 830327.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VWA1NM_022834.5 linkc.62_71dupGCGCGGAGCG p.Gly25ArgfsTer74 frameshift_variant, splice_region_variant Exon 1 of 3 ENST00000476993.2 NP_073745.2 Q6PCB0-1
VWA1NM_199121.3 linkc.62_71dupGCGCGGAGCG p.Gly25ArgfsTer53 frameshift_variant, splice_region_variant Exon 1 of 3 NP_954572.2 Q6PCB0-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VWA1ENST00000476993.2 linkc.62_71dupGCGCGGAGCG p.Gly25ArgfsTer74 frameshift_variant, splice_region_variant Exon 1 of 3 1 NM_022834.5 ENSP00000417185.1 Q6PCB0-1
VWA1ENST00000471398.1 linkc.62_71dupGCGCGGAGCG p.Gly25ArgfsTer14 frameshift_variant, splice_region_variant Exon 1 of 2 3 ENSP00000464343.1 J3QRR0
VWA1ENST00000338660.5 linkc.62_71dupGCGCGGAGCG p.Gly25ArgfsTer53 frameshift_variant, splice_region_variant Exon 1 of 3 2 ENSP00000423404.1 Q6PCB0-3
VWA1ENST00000495558.1 linkc.-33+664_-33+673dupGCGCGGAGCG intron_variant Intron 1 of 1 2 ENSP00000463643.1 J3QLP3

Frequencies

GnomAD3 genomes
AF:
0.000669
AC:
100
AN:
149504
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000510
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000665
Gnomad ASJ
AF:
0.000292
Gnomad EAS
AF:
0.000195
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000956
Gnomad OTH
AF:
0.000971
GnomAD4 exome
AF:
0.000969
AC:
1020
AN:
1052936
Hom.:
1
Cov.:
31
AF XY:
0.000991
AC XY:
507
AN XY:
511496
show subpopulations
Gnomad4 AFR exome
AF:
0.000749
Gnomad4 AMR exome
AF:
0.000455
Gnomad4 ASJ exome
AF:
0.0000841
Gnomad4 EAS exome
AF:
0.0000715
Gnomad4 SAS exome
AF:
0.0000772
Gnomad4 FIN exome
AF:
0.0000549
Gnomad4 NFE exome
AF:
0.00106
Gnomad4 OTH exome
AF:
0.00105
GnomAD4 genome
AF:
0.000668
AC:
100
AN:
149610
Hom.:
0
Cov.:
32
AF XY:
0.000644
AC XY:
47
AN XY:
73002
show subpopulations
Gnomad4 AFR
AF:
0.000509
Gnomad4 AMR
AF:
0.000664
Gnomad4 ASJ
AF:
0.000292
Gnomad4 EAS
AF:
0.000196
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000956
Gnomad4 OTH
AF:
0.000961

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Neuronopathy, distal hereditary motor, autosomal recessive 7 Pathogenic:5
Feb 05, 2024
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Apr 26, 2022
Fulgent Genetics, Fulgent Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 17, 2023
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

May 22, 2024
Neurogenomics Lab, Neuroscience Institute, University Of Cape Town
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

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
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

VWA1: PVS1, PM2, PM3 -

Jan 12, 2023
Clinical Genetics Laboratory, Skane University Hospital Lund
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Neuromuscular disease Pathogenic:1
Jan 01, 2020
Section for Clinical Neurogenetics, University of Tübingen
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

VWA1-related disorder Pathogenic:1
Sep 16, 2022
PreventionGenetics, part of Exact Sciences
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs749383814; hg19: chr1-1371178; API