A single-center study on 140 patients with cerebral cavernous malformations: 28 new pathogenic variants and functional characterization of a PDCD10 large deletion

Abstract

Cerebral cavernous malformation (CCM) is a capillary malformation arising in the central nervous system. CCM may occur sporadically or cluster in families with autosomal dominant transmission, incomplete penetrance, and variable expressivity. Three genes are associated with CCM KRIT1, CCM2, and PDCD10. This work is a retrospective single-center molecular study on samples from multiple Italian clinical providers. From a pool of 317 CCM index patients, we found germline variants in either of the three genes in 80 (25.2%) probands, for a total of 55 different variants. In available families, extended molecular analysis found segregation in 60 additional subjects, for a total of 140 mutated individuals. From the 55 variants, 39 occurred in KRIT1 (20 novel), 8 in CCM2 (4 novel), and 8 in PDCD10 (4 novel). Effects of the three novel KRIT1 missense variants were characterized in silico. We also investigated a novel PDCD10 deletion spanning exon 4-10, on patient's fibroblasts, which showed significant reduction of interactions between KRIT1 and CCM2 encoded proteins and impaired autophagy process. This is the largest study in Italian CCM patients and expands the known mutational spectrum of KRIT1, CCM2, and PDCD10. Our approach highlights the relevance of seeking supporting information to pathogenicity of new variants for the improvement of management of CCM.

Response to: Concern regarding classification of c.703G>A/p.Gly235Arg as a novel missense variant in KRIT1 gene

“…Thanks to the annotation by Battistini and Ricci (2020), we recognized that the variant KRIT1 c.703G>A, p.(Gly235Arg) reported as ''novel'' in our manuscript (Nardella et al, 2018), has been previously published in (Cerase et al, 2010). We apologize for this mistake which was likely facilitated by the absence of the variant Such uncertainties on the potential effect of this variant on the splicing process prompt us to maintain prudence in assuming this variant as affecting splicing (i.e., splicing variant).…”

Response to: Concern regarding classification of c.703G>A/p.Gly235Arg as a novel missense variant in KRIT1 gene

“…Thanks to the annotation by Battistini and Ricci (2020), we recognized that the variant KRIT1 c.703G>A, p.(Gly235Arg) reported as ''novel'' in our manuscript (Nardella et al, 2018), has been previously published in (Cerase et al, 2010). We apologize for this mistake which was likely facilitated by the absence of the variant Such uncertainties on the potential effect of this variant on the splicing process prompt us to maintain prudence in assuming this variant as affecting splicing (i.e., splicing variant).…”

Molecular genetic features and clinical manifestations in Chinese familial cerebral cavernous malformation: from a novel KRIT1/CCM1 mutation (c.1119dupT) to an overall view

“…In Chinese fCCMs carrying KRIT1/CCM1 variants, all these variants result in the functional deletion or insufficiency of the C-terminal FERM (a band four-point-one, ezrin, radixin, moesin) domain of the KRIT1 protein ( Figure 5C ). KRIT1 binds to microtubules, and when activated RAP1 binds to the FERM domain, KRIT1 translocates to adherens junctions and binds β-catenin ( Francalanci et al, 2009 ; Nardella et al, 2018 ). However, as previously reported ( Liu et al, 2011 ), the depletion of KRIT1-RAP1 interaction caused a deleterious decreased endothelial barrier function.…”

Novel Pathogenic Variants in a Cassette Exon of CCM2 in Patients With Cerebral Cavernous Malformations

“…A novel pathogenic 1-bp duplication [LRG_664t2: c.169dupA; LRG_664p2: p.(Arg57Lysfs * 8)] was detected in the blood sample of the index patient of family 2 (Figure 2C) and a 2-bp deletion [LRG_664t2: c.134_135delTG; LRG_664p2: p.(Val45Glyfs * 6)] was identified in family 3 (Figure 2D). The latter had previously been described in an Italian CCM family (17) and was listed as likely pathogenic in the ClinVar database (ClinVar-ID: 590648). Unfortunately, a blood sample from the maternal aunt of the index patient in family 2 was not available to test for the CCM2 variant.…”

Response to: Concern regarding classification of c.703G>A/p.Gly235Arg as a novel missense variant in KRIT1 gene

“…Thanks to the annotation by Battistini and Ricci (2020), we recognized that the variant KRIT1 c.703G>A, p.(Gly235Arg) reported as ''novel'' in our manuscript (Nardella et al, 2018), has been previously published in (Cerase et al, 2010). We apologize for this mistake which was likely facilitated by the absence of the variant Such uncertainties on the potential effect of this variant on the splicing process prompt us to maintain prudence in assuming this variant as affecting splicing (i.e., splicing variant).…”

Molecular genetic features and clinical manifestations in Chinese familial cerebral cavernous malformation: from a novel KRIT1/CCM1 mutation (c.1119dupT) to an overall view

“…In Chinese fCCMs carrying KRIT1/CCM1 variants, all these variants result in the functional deletion or insufficiency of the C-terminal FERM (a band four-point-one, ezrin, radixin, moesin) domain of the KRIT1 protein ( Figure 5C ). KRIT1 binds to microtubules, and when activated RAP1 binds to the FERM domain, KRIT1 translocates to adherens junctions and binds β-catenin ( Francalanci et al, 2009 ; Nardella et al, 2018 ). However, as previously reported ( Liu et al, 2011 ), the depletion of KRIT1-RAP1 interaction caused a deleterious decreased endothelial barrier function.…”

Novel Pathogenic Variants in a Cassette Exon of CCM2 in Patients With Cerebral Cavernous Malformations

“…A novel pathogenic 1-bp duplication [LRG_664t2: c.169dupA; LRG_664p2: p.(Arg57Lysfs * 8)] was detected in the blood sample of the index patient of family 2 (Figure 2C) and a 2-bp deletion [LRG_664t2: c.134_135delTG; LRG_664p2: p.(Val45Glyfs * 6)] was identified in family 3 (Figure 2D). The latter had previously been described in an Italian CCM family (17) and was listed as likely pathogenic in the ClinVar database (ClinVar-ID: 590648). Unfortunately, a blood sample from the maternal aunt of the index patient in family 2 was not available to test for the CCM2 variant.…”

Response to: Concern regarding classification of c.703G>A/p.Gly235Arg as a novel missense variant in KRIT1 gene

“…Thanks to the annotation by Battistini and Ricci (2020), we recognized that the variant KRIT1 c.703G>A, p.(Gly235Arg) reported as ''novel'' in our manuscript (Nardella et al, 2018), has been previously published in (Cerase et al, 2010). We apologize for this mistake which was likely facilitated by the absence of the variant Such uncertainties on the potential effect of this variant on the splicing process prompt us to maintain prudence in assuming this variant as affecting splicing (i.e., splicing variant).…”

Molecular genetic features and clinical manifestations in Chinese familial cerebral cavernous malformation: from a novel KRIT1/CCM1 mutation (c.1119dupT) to an overall view

“…In Chinese fCCMs carrying KRIT1/CCM1 variants, all these variants result in the functional deletion or insufficiency of the C-terminal FERM (a band four-point-one, ezrin, radixin, moesin) domain of the KRIT1 protein ( Figure 5C ). KRIT1 binds to microtubules, and when activated RAP1 binds to the FERM domain, KRIT1 translocates to adherens junctions and binds β-catenin ( Francalanci et al, 2009 ; Nardella et al, 2018 ). However, as previously reported ( Liu et al, 2011 ), the depletion of KRIT1-RAP1 interaction caused a deleterious decreased endothelial barrier function.…”

Novel Pathogenic Variants in a Cassette Exon of CCM2 in Patients With Cerebral Cavernous Malformations

“…A novel pathogenic 1-bp duplication [LRG_664t2: c.169dupA; LRG_664p2: p.(Arg57Lysfs * 8)] was detected in the blood sample of the index patient of family 2 (Figure 2C) and a 2-bp deletion [LRG_664t2: c.134_135delTG; LRG_664p2: p.(Val45Glyfs * 6)] was identified in family 3 (Figure 2D). The latter had previously been described in an Italian CCM family (17) and was listed as likely pathogenic in the ClinVar database (ClinVar-ID: 590648). Unfortunately, a blood sample from the maternal aunt of the index patient in family 2 was not available to test for the CCM2 variant.…”