rs796943858

Positions:

• chr21-43774279-GGA-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Strong PM2 PP5_Very_Strong

The NM_000100.4(CSTB):​c.218_219del​(p.Leu73ProfsTer3) variant causes a frameshift change. The variant allele was found at a frequency of 0.000224 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. L73L) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000053 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00024 (0 hom.)
• Consequence: CSTB NM_000100.4 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10 O:1
• Conservation: PhyloP100: 5.03

Genes affected

CSTB (HGNC:2482): (cystatin B) The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and kininogens. This gene encodes a stefin that functions as an intracellular thiol protease inhibitor. The protein is able to form a dimer stabilized by noncovalent forces, inhibiting papain and cathepsins l, h and b. The protein is thought to play a role in protecting against the proteases leaking from lysosomes. Evidence indicates that mutations in this gene are responsible for the primary defects in patients with progressive myoclonic epilepsy (EPM1). One type of mutation responsible for EPM1 is the expansion in the promoter region of this gene of a CCCCGCCCCGCG repeat from 2-3 copies to 30-78 copies. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.266 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 21-43774279-GGA-G is Pathogenic according to our data. Variant chr21-43774279-GGA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55960.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-43774279-GGA-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSTB	NM_000100.4	c.218_219del	p.Leu73ProfsTer3	frameshift_variant	3/3	ENST00000291568.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSTB	ENST00000291568.7	c.218_219del	p.Leu73ProfsTer3	frameshift_variant	3/3	1	NM_000100.4	P1
CSTB	ENST00000639959.1	c.85_86del	p.Leu29ProfsTer3	frameshift_variant	2/2	5
CSTB	ENST00000640406.1	c.*293_*294del		3_prime_UTR_variant	2/2	2
CSTB	ENST00000675996.1	n.643_644del		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.0000526 AC: 8 AN: 152218 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251470 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135922

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000440

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000241 AC: 353 AN: 1461870 Hom.: 0 AF XY: 0.000239 AC XY: 174 AN XY: 727234

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000308

Gnomad4 OTH exome AF: 0.000149

GnomAD4 genome AF: 0.0000526 AC: 8 AN: 152218 Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4 AN XY: 74362

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000735

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000302

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Unverricht-Lundborg syndrome Pathogenic:5 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 30, 2022	Variant summary: CSTB c.218_219delTC (p.Leu73ProfsX3) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 2.5e-05 in 282872 control chromosomes (gnomAD). c.218_219delTC has been reported in the literature in individuals affected with Unverricht-Lundborg Syndrome (e.g. Lafreniere_1997, Lalioti_1997, Bespalova_1997). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating protein function, and found that the variant does not localize to the lysosomes which may contribute to misfunction (Alakurtti_2005). Five ClinVar submitters have assessed the variant since 2014: one classified the variant as likely pathogenic, and four as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 01, 2005	- -
Likely pathogenic, no assertion criteria provided	literature only	Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 23, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jan 27, 2016	The c.218_219delTC (p.Leu73Profs*3) frameshift variant in the CSTB gene has been previously reported as heterozygous in three affected individuals with autosomal recessive Myoclonic epilepsy of Unverricht and Lundborg (Bespalova et al., 1997; Lafrenière et al., 1997; Lalioti et al., 1997). This frameshift variant is predicted to cause a protein termination in exon 3 (out of a total of 3 exons in the coding sequence). The C-terminal end of the protein, which is truncated by this variant, is important for normal protein function (Pol and Bjork, 1999). Nonsense mutations in the CSTB gene have been reported as pathogenic (Gln47*, Arg68*), and thus, loss of function is a known mechanism of disease. Additionally, in vitro functional studies have shown this variant leads to abnormal localization of the protein within the cell, similar to other pathogenic variants (Cipollini et al., 2008; Alakurtti et al., 2005). This c.218_219delTC has been reported at low frequency in the population databases (Exome Sequencing Project [ESP] = NA, 1000 Genomes = NA, and ExAC = 0.001%) and is predicted to be located in an evolutionarily conserved region (GERP = 5.46). Therefore, this collective evidence supports the classification of the c.218_219delTC (p.Leu73Profs*3) as a recessive Likely Pathogenic variant for Myoclonic epilepsy of Unverricht and Lundborg. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 31, 2023	PP4, PM2, PS3, PS4_moderate, PVS1_strong -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 12, 2024	Published functional studies suggest that the variant does not localize to lysosomes as compared to unaffected controls (PMID: 15483648, 17920138); Frameshift variant predicted to result in protein truncation as the last 26 amino acids are replaced with 2 different amino acids, although loss-of-function variants have not been reported downstream of this position in the protein; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 9054946, 9342192, 7543407, 17003839, 30669344, 17920138, 31440721, 38247861, 9012407, 15483648) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 16, 2021	This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in at least one individual with clinical features associated with this gene. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2022

The c.218_219delTC (p.L73Pfs*3) alteration, located in exon 3 (coding exon 3) of the CSTB gene, consists of a deletion of 2 nucleotides from position 218 to 219, causing a translational frameshift with a predicted alternate stop codon after 3 amino acids. This alteration occurs at the 3' terminus of the CSTB gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 26 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function. Based on data from gnomAD, this allele has an overall frequency of 0.003% (7/282872) total alleles studied. The highest observed frequency was 0.005% (6/129176) of European (non-Finnish) alleles. This mutation has been reported in three unrelated individuals with Unverricht-Lundborg disease (EPM1) (Bespalova, 1997; Lafrenière, 1997; Lalioti, 1997). A second mutation (expansion of the dodecamer repeat) was identified in one of the individuals. Studies of bovine CSTB have shown that some of the C-terminal residues affected by this truncation are important for protein function (Pol, 1999). In addition, this protein truncation is predicted to be structurally destabilizing and to disrupt binding of target proteins (Ambry internal data; Stubbs, 1990; Jenko Kokalj, 2007). Functional analysis demonstrated that levels of CSTB mRNA were significantly decreased in cells from patients heterozygous for the CSTB c.218_219delTC (p.L73Pfs*3) alteration compared to unaffected individuals (Lafrenière, 1997; Bespalova, 1997). When the L73Pfs*3 protein was expressed in vitro, the mutant protein had diffuse distribution in the cytoplasm and nucleus and did not colocalize with lysosomes (Alakurtti, 2005). Based on the available evidence, this alteration is classified as pathogenic. -

Progressive myoclonic epilepsy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 21, 2023

This sequence change creates a premature translational stop signal (p.Leu73Profs*3) in the CSTB gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 26 amino acid(s) of the CSTB protein. This variant is present in population databases (rs796943858, gnomAD 0.005%). This premature translational stop signal has been observed in individual(s) with progressive myoclonus epilepsy type 1 (PMID: 9012407, 9054946, 9342192). This variant is also known as c.313_314del2, del2399TC, and 2404ΔTC. ClinVar contains an entry for this variant (Variation ID: 55960). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects CSTB function (PMID: 9342192, 15483648, 17920138). This variant disrupts the p.Leu73 amino acid residue in CSTB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10441148). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs796943858; hg19: chr21-45194160;