ClinVar Genomic variation as it relates to human health

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Variant summary: RBM8A c.-21G>A is located in the untranslated mRNA region upstream of the initiation codon. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.018 in 237842 control chromosomes in the gnomAD database, including 61 homozygotes. c.-21G>A has been reported in the literature in multiple individuals affected with Radial Aplasia-Thrombocytopenia Syndrome. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and showed that variant resulted in decreased promoter activity (Albers_2012). Twelve clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The RBM8A c.-21G>A (p.?) variant is a pathogenic variant that is located in the 5' noncoding, untranslated region (5' UTR) of the RBM8A gene. This variant is associated with reduced RBM8A gene activity, and is a mild (hypomorphic) variant that is associated with thrombocytopenia absent radius (TAR) syndrome only in the presence of a more severe, loss-of-function RBM8A variant in trans (PMID: 22366785; 24053387).

This variant has been reported in the literature in numerous individuals with thrombocytopenia-absent radius (TAR) syndrome, most often as a compound heterozygote in trans with a recurrent 200kb deletion (Selected publications: Albers 2012 PMID: 22366785; Bottillo 2013 PMID: 24053387; Bastida 2018 PMID: 28983057; Boussion 2020 PMID: 32227665) and is present in the GeneReviews entry for this gene (Toriello 2016 PMID: 20301781). Of note, individuals who carry this variant in the homozygous state have typically not been found in association with disease (Toriello 2016 PMID: 20301781). This variant is present in the Genome Aggregation Database (Highest reported MAF: 2.8% [3411/122966], including in 64 total homozygotes (https://gnomad.broadinstitute.org/variant/1-145507646-G-A?dataset=gnomad_r2_1). This variant is also present in ClinVar, with several labs classifying this variant as Pathogenic (Variation ID: 30464). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant occurs in the 5' UTR of this gene and does not change the coding sequence; however, literature suggests that this variant affects promoter activity and functions as a hypomorphic allele (Albers 2012 PMID: 22366785). In summary, although this variant occurs at a high minor allele frequency, there is significant evidence suggesting a disease-causing impact of this variant and it is thus classified as pathogenic, but may be best regarded as a a hypomorphic allele.

The RBM8A c.-21G>A variant is located in the 5' untranslated region. The c.-21G>A substitution is found in apparently unaffected individuals at frequencies over 2.7% (Albers et al. 2012. PubMed ID: 22366785; see also gnomAD database). However, significant evidence suggests the c.-21G>A substitution is a “functional polymorphism” and that when paired with a null RBM8A allele, such as a large 1q21.1 deletion identified in most TAR patients, is likely a cause of thrombocytopenia with absent radius (TAR) (Albers et al. 2012. PubMed ID: 22366785; Bottillo et al. 2013. PubMed ID: 24053387). Using a cell-based, biochemical assay, studies from Albers et al. 2012 show that the c.-21G>A substitution may decrease transcription of a reporter gene and therefore, when found in patients also harboring a null RBM8A allele, may result in reduction of RBM8A protein to levels below a critical threshold required by some cell types. In summary, the c.-21G>A variant has been found in a high proportion of patients with TAR who also have a large deletion on the opposite allele that includes the RBM8A gene. However, individuals that are homozygous for the c.-21 G>A variant are not expected to have features of TAR syndrome (Bottillo et al. 2013. PubMed ID: 24053387; see also gnomAD database). Based on the collective evidence, we interpret this variant as pathogenic.

The c.-21G>A variant in the RBM8A gene is a reported cause of thrombocytopenia absent radius syndrome (Albers et al., 2012; Boussion et al., 2020). This variant in the homozygous state does not cause thrombocytopenia absent radius syndrome; however, this variant in conjunction with a loss of function variant is a common cause of thrombocytopenia absent radius syndrome. The c.-21G>A variant was determined to be in trans with a pathogenic variant (1q21.1 deletion) consistent with autosomal recessive inheritance (Albers et al., 2012; Boussion et al., 2020). The presence of this variant with an established disease-causing variant on the opposite allele increases suspicion for its pathogenicity. This variant has been identified in 3,411/122,966 European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, its frequency is consistent with a recessive carrier frequency for a mild allele. Well-established in vitro functional studies of the c.-21G>A variant strongly suggest it reduces protein expression that is sufficient to be disease-causing (Albers et al., 2012; Boussion et al., 2020). These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.-21G>A variant as pathogenic for autosomal recessive thrombocytopenia absent radius (TAR) syndrome based on the information above. [ACMG evidence codes used: PS3; PM3_verystrong]

This variant occurs in a non-coding region of the RBM8A gene. It does not change the encoded amino acid sequence of the RBM8A protein. This variant is present in population databases (rs139428292, gnomAD 2.8%), including at least one homozygous and/or hemizygous individual. This variant has been observed in individual(s) with TAR Syndrome (PMID: 22366785, 24220582, 27320760). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 30464). Studies have shown that this variant alters RBM8A gene expression (PMID: 22366785). In summary, this variant is reported to cause disease. However, as this variant is associated with a lower penetrance than other pathogenic alleles in the RBM8A gene, it has been classified as Pathogenic (low penetrance).

PS3, PS4_MOD - It has been reported in ClinVar as Pathogenic by other laboratories (Variation ID: 30464).

Published functional studies suggest a damaging effect due to disruption of transcription factor binding and reduced transcription of RBM8A, indicating that this is a hypomorphic allele (PMID: 22366785); Nucleotide is not conserved across species and the substitution has no predicted effect on splicing; This variant is associated with the following publications: (PMID: 25813282, 24053387, 28556904, 22366785, 32981126, 27320760, 24220582, 30385887, 30609409, 29595812, 20301781, 32227665, 28983057, 32333414, 28857120, 36939041, 34323054, 36077017)

The heterozygous c.-21G>A variant in RBM8A was identified by our study in one individual in the compound heterozygous state, with a copy number variant, with Thrombocytopenia Absent Radius syndrome (TAR). This variant has been identified in 1.812% (4778/2263746) of chromosomes, including 63 homozygous individuals, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs139428292). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role in the compound heterozygous state. The c.-21G>A variant in RBM8A has been reported in the heterozygous state, with a deletion or frameshift variant, in 39 individuals with TAR (PMID: 22366785). Trio exome analysis in the literature showed this variant to be de novo in at least 8 individuals (PMID: 22366785). The presence of this variant in combination with a reported pathogenic variant and in an individual with TAR increases the likelihood that the c.-21G>A variant is pathogenic in the compound heterozygous state, though not the homozygous state. This variant has also been reported pathogenic and likely pathogenic in ClinVar (Variation ID: 30464). The c.-21G>A variant is pathogenic based off of our findings, multiple de novo reports in the literature, and ClinVar. ACMG/AMP Criteria applied: PM3_Strong, PM6_Strong (Richards 2015).

PP4, PM3, PS3

The c.-21G>A variant in RBM8A has been reported in the compound heterozygous state in numerous individuals with thrombocytopenia with absent radius (TAR) syndrome. The majority of these individuals had a submicroscopic deletion encompassing the RBM8A gene on the other allele, while the remaining cases had different truncating variants on the opposite allele (Albers 2012 PMID: 22366785, Bottillo 2013 PMID: 24053387, Manukjan 2017 PMID: 28857120). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID #30464) and has been identified in 2.9% (1979/68026) of European chromosomes, including 27 homozygotes in gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role in the compound heterozygous state. This variant is located in the 5'UTR of the RBM8A gene and does not affect the coding sequence. In vitro studies suggest that it affects promoter activity and may lead to reduced gene expression, functioning as a hypomorphic allele (Albers 2012 PMID: 22366785). Compound heterozygosity for a hypomorph (this variant) and a loss of function variant in RBM8A is strongly associated with TAR syndrome; however, individuals that are homozygous for the c.-21G>A variant are not expected to have features of TAR syndrome. In summary, despite its frequency in the general population, this variant meets criteria to be pathogenic for autosomal recessive TAR syndrome when in compound heterozygosity with another more severe loss of function RBM8A variant. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3_Moderate.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Thrombocytopaenia-absent radius syndrome (TARS, MIM#605313). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0217 - Non-coding variant with known effect. This variant results in reduced expression of the Y14 protein (PMID: 22366785). (SP) 0253 - This variant is hemizygous. (I) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v2: 4703 heterozygotes, 64 homozygotes). Individuals homozygous for this variant do not have features of TAR syndrome. (PMID: 20301781). (I) 0311 - An alternative nucleotide change at the same position has been observed in gnomAD (v2: 1 heterozygote, 0 homozygotes). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This is a recurrent pathogenic variant commonly reported in trans with a 1q21.1 deletion in patients with TARS (PMID: 22366785, PMID 28857120, PMID 32227665 and ClinVar). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. The variant results in decreased RBM8A promoter activity and reduced expression of the encoded protein (Y14) in platelets from TARS patients (PMID: 22366785). (SP) 1101 - Very strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

RBM8A: PS4:Moderate, PS3:Supporting

Converted during submission to Pathogenic.