ClinVar Genomic variation as it relates to human health

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000001260, PMID:16845400, PS1_S). Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product(PMID: 19015152, 21177854, PS3_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.709, PP3_P). A missense variant is a common mechanism associated with Aicardi-Goutieres syndrome 3 (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000092, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

A homozygous missense variation in exon 2 of the RNASEH2C gene that results in the amino acid substitution of Valine for Arginine at codon 69 was detected. The observed variant c.205C>T (p.Arg69Trp) has not been reported in the 1000 genomes and ExAC databases. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic.

A Homozygote Missense variant c.205C>T in Exon 2 of the RNASEH2C gene that results in the amino acid substitution p.Arg69Trp was identified. The observed variant has allele frequency of 0.00009/0.00 % in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic/LikelyPathogenic(ClinVar ID: 1260). Functional studies demonstrate that R69W is associated with decreased enzyme activity and reduced thermal stability of RNaseH2 (Chon H et al., 2009). c.205C>T has been reported in the literature as a homozygous genotype in multiple individuals affected with Aicardi Goutieres Syndrome and is reported as a frequent founder mutation of Asian origin (Kaur P et al., 2021 and Rice G et al., 2007). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 69 of the RNASEH2C protein (p.Arg69Trp). This variant is present in population databases (rs78635798, gnomAD 0.07%). This missense change has been observed in individuals with Aicardi-Goutieres syndrome (PMID: 16845400, 23322642, 29150899, 29239743). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1260). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on RNASEH2C function (PMID: 19015152, 19034401, 31529068). For these reasons, this variant has been classified as Pathogenic.

This variant is interpreted as a Likely Pathogenic, for Aicardi-Goutieres syndrome 3, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:23322642) (PMID:16845400). PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => Recurrent mutation observed in multiple patients. (PMID:17846997,16845400,20131292,23322642,29150899).

Variant summary: RNASEH2C c.205C>T (p.Arg69Trp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 9.2e-05 in 250836 control chromosomes, predominantly at a frequency of 0.00072 within the South Asian subpopulation in the gnomAD database. c.205C>T has been reported in the literature as a homozygous genotype in multiple individuals affected with Aicardi Goutieres Syndrome and is reported as a frequent founder mutation of Asian origin (example, Rice_2007, Vogt_2013, Kaur_2021). 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, however, does not allow convincing conclusions about the variant effect (Nishimura_2019). Nine 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.

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 Aicardi-Goutieres syndrome 3 (MIM#610329). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2) (23 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated ribonuclease H2 non-catalytic subunit (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity. It has been reported in more than 30 patients in a homozygous state and is likely a founder mutation in the South Asian population (ClinVar, PMIDs: 17846997, 20131292, 29150899). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. This variant causes a decrease in RNase enzyme activity and stability (PMIDs: 19015152, 31529068). (SP) 1101 - Very strong and specific phenotype match for this individual. (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Published functional studies demonstrate that R69W is associated with decreased enzyme activity and reduced thermal stability of RNaseH2 (Chon et al., 2009; Reijns et al., 2011); This variant is associated with the following publications: (PMID: 25604658, 31529068, 29239743, 17846997, 21177854, 19034401, 19015152, 26456534, 23322642, 20131292, 16845400, 29150899, 27391121, 24123366, 29302074, 32180488)

The missense c.205C>T (p.Arg69Trp) variant in RNASEH2C gene has been reported in homozygous state in individuals affected with Aicardi-Goutieres syndrome 3 (Nishimura T et al. 2019; Hebbar M et al. 2018). Functional studies demonstrate that R69W is associated with decreased enzyme activity and reduced thermal stability of RNaseH2 (Reijns et al., 2011). The p.Arg69Trp variant has allele frequency of 0.01% in gnomAD Exomes. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). The reference amino acid p.Arg69Trp in RNASEH2C is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Multiple lines of computational evidence (Polyphen-damaging, SIFT-damaging and Mutation Taster- disease causing) predict a damaging effect on protein structure and function for this variant. The amino acid Arginine at position 69 is changed to a Tryptophan changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.