ClinVar Genomic variation as it relates to human health

PS3_moderate;PM2_supporting;PM3_moderate;PP5_supporting;BP4_supporting

The c.82A>C (p.S28R) alteration is located in exon 1 (coding exon 1) of the DONSON gene. This alteration results from an A to C substitution at nucleotide position 82, causing the serine (S) at amino acid position 28 to be replaced by an arginine (R). The c.1466A>C (p.K489T) alteration is located in exon 9 (coding exon 9) of the DONSON gene. This alteration results from an A to C substitution at nucleotide position 1466, causing the lysine (K) at amino acid position 489 to be replaced by a threonine (T). The p.S28R and p.K489T alterations have been observed to be linked in cis and form a haplotype which also includes an intronic c.786-33A>G change (Reynolds, 2017). Based on the available evidence, the DONSON c.[82A>C;1466A>C] (p.[S28R;K489T]) haplotype is classified as pathogenic._x000D_ _x000D_ VUS if seen without c.82A>C Based on data from gnomAD, the C allele has an overall frequency of 0.09% (266/282866) total alleles studied. The highest observed frequency was 0.72% (75/10370) of Ashkenazi Jewish alleles. This haplotype including p.S28R, p.K489T, and c.786-33A>G was detected in the heterozygous state in trans with truncating variants in five unrelated patients with microcephalic dwarfism (Reynolds, 2017). The p.S28R and p.K489T variants were both identified in the homozygous state in an individual from a consanguineous family with spondylo-epi-metaphyseal dysplasia (SEMD) who had many additional homozygous variants in other genes as well (Guo, 2017). The p.S28 and p.K489 amino acids are not well conserved in available vertebrate species. Of the three variants in the common haplotype, only p.K489T was found to have a negative effect in functional studies. Functional analysis demonstrated the p.K489T alteration reduced protein levels and was unable to complement the loss of endogenous DONSON during replication fork stalling (Reynolds, 2017). The p.S28R and p.K489T alterations are predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is 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 microcephaly, short stature, and limb abnormalities (MIM#617604) and microcephaly-micromelia syndrome (MIM#251230). (I) 0106 - This gene is associated with autosomal recessive disease. However there has been one previous report of an individual with femoral facial syndrome who was only heterozygous for one DONSON variant (PMID: 31407851). (I) 0200 - Variant is predicted to result in a missense amino acid change from lysine to threonine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (264 heterozygotes, 1 homozygote). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (220 heterozygotes, 2 homozygotes). (I) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. However a variant with a lower Grantham score, p.(Lys489Arg), has been reported as benign once by a clinical laboratory in ClinVar. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been observed in eleven individuals with DONSON-related conditions and in at least seven it was observed on an ancestral haplotype, in cis with two other DONSON variants, p.(Ser28Arg) and c.786-33A>G, variants that are not considered to be pathogenic (ClinVar, PMID: 28191891). This variant has also previously been classified as a VUS or benign by clinical laboratories in ClinVar. (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Western blot and immunoblot studies have shown this variant causes reduced DONSON protein levels (PMID: 28191891). (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Variant summary: DONSON c.1466A>C (p.Lys489Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00097 in 251470 control chromosomes in the gnomAD database, including one homozygote. This frequency is not significantly higher than estimated for a pathogenic variant in DONSON causing Microcephaly, Short Stature, And Limb Abnormalities, allowing no conclusion about variant significance. c.1466A>C has been reported in the literature in individuals affected with Microcephaly, Short Stature, And Limb Abnormalities (Chong_2015, Reynolds_2017). In addition, this variant was found in a haplotype defined by 3 co-segregating variants (c.82A>C:p.Ser28Arg; c.78633A>G; c.1466A>C:p.Lys489Thr) (Reynolds_2017). These reports do not provide unequivocal conclusions about association of the variant with Microcephaly, Short Stature, And Limb Abnormalities. At least one publication reports experimental evidence evaluating an impact on protein function (Reynolds_2017). The following publications have been ascertained in the context of this evaluation (PMID: 27040692, 28191891). ClinVar contains an entry for this variant (Variation ID: 431445). Based on the evidence outlined above, the variant was classified as uncertain significance.

DONSON: BP4

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).