ClinVar Genomic variation as it relates to human health

The c.3286 C>T (p.Arg1096Cys) variant in POLG is seen at an allele frequency of 0.00001 in gnomAd and 0.00002 in ExAC with no homozygotes (PM2). This variant has a Revel score of 0.837 (PP3). There are 7 cases in the literature reported with an Alpers phenotype in individuals who are homozygous for the c.3286 C>T (p.Arg1096Cys) (PM3_strong; PMID:21305355; PMID:21880868; PMID:18546365). There are also 6 cases reported with other pathogenic variants with phasing unknown 2 siblings reported compound heterozygous with Thr914Pro, another reported with Trp748Ser, another cases with Leu591Phe, another case with Ala467Thr, and another case with Gly848Ser. Each case was reported with POLG related disease with Alpers, liver related disease, and other neurological phenotypes (PM3_strong; PMID:18487244; PMID:30021052; PMID:24265579; PMID:27111573; PMID:21880868). In summary, this variant meets criteria to be classified as likely pathogenic for mitochondrial disease inherited in an autosomal recessive manner. ntDNA ACMG/AMP criteria for POLG applied: PM2, PP3, PM3_strong

The NM_002693.2:c.3286C>T (NP_002684.1:p.Arg1096Cys) [GRCH38: NC_000015.10:g.89318737G>A] variant in POLG gene is interpretated to be a Pathogenic based on ACMG guidelines (PMID: 25741868). This variant has been reported in PMID:12707443 ; 21305355 . This variant meets the following evidence codes reported in the ACMG-guideline. PS1:This variation causes same amino-acid change as an established pathogenic variant. PS3:Well established functional studies show a deleterious effect on POLG. PM2:This variant is absent in key population databases. PM3:Detected in trans with a pathogenic variant for Mitochondrial DNA depletion syndrome 4A (Alpers type) which is a recessive disorder. PP1:This variant is co-segregated with Mitochondrial DNA depletion syndrome 4A (Alpers type) in multiple affected family members. PP4:Patient's phenotype or family history is highly specific for POLG. Based on the evidence criteria codes applied, the variant is suggested to be Pathogenic.

Reported previously in multiple patients with Alpers syndrome, a clinical presentation suggestive of POLG deficiency, or progressive external ophthalmoplegia (arPEO) and peripheral neuropathy, who were either homozygous for the R1096C variant (Mohamed et al., 2011; Wong et al, 2008; Tang et al., 2011; Ashley et al. 2008) or compound heterozygous for the R1096C variant and another pathogenic variant (Tang et al., 2011; Ashley et al., 2008; Lax et al., 2012); Functional studies have demonstrated that the R1096C variant results in a decreased catalytic efficiency in incorporating correct dNTP into DNA (Sohl et al., 2013); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28471437, 29655203, 22189570, 24265579, 21305355, 12707443, 25129007, 23545419, 19578034, 25786813, 20164463, 21880868, 18487244, 23208208, 21138766, 29474836, 30167885, 31521625, 31130284)

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1096 of the POLG protein (p.Arg1096Cys). This variant is present in population databases (rs201732356, gnomAD 0.004%). This missense change has been observed in individuals with autosomal recessive POLG-related disease (PMID: 21305355, 21880868, 22189570, 24265579, 28471437, 30167885). This variant has been reported in individual(s) with autosomal dominant progressive external ophthalmoplegia (PMID: 12707443); however, the role of the variant in this condition is currently unclear. ClinVar contains an entry for this variant (Variation ID: 206556). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt POLG protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects POLG function (PMID: 20185557, 23208208). This variant disrupts the p.Arg1096 amino acid residue in POLG. Other variant(s) that disrupt this residue have been observed in individuals with POLG-related conditions (PMID: 16621917, 19752458), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.84; 3Cnet: 0.89). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000206556). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals (PMID: 18487244 , 18546365 , 21305355 , 21880868 , 24265579 , 27111573 , 30021052). Different missense changes at the same codon (p.Arg1096Gly, p.Arg1096His, p.Arg1096Leu) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000206555 , VCV000206557 , VCV000206559). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

Variant summary: POLG c.3286C>T (p.Arg1096Cys) results in a non-conservative amino acid change located in the DNA-directed DNA polymerase, family A, palm domain (IPR001098) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251284 control chromosomes. c.3286C>T has been reported in the literature in multiple individuals affected with autosomal recessive POLG-related disorders and in at least one patient with autosomal dominant progressive external ophthalmoplegia (e.g. Tang_2011, Agostino_2003). These data indicate that the variant is very likely to be associated with disease. A different variant affecting the same codon has been classified as pathogenic by our lab (c.3287G>A, p.Arg1096His), supporting the critical relevance of codon 1096 to POLG protein function. At least one publication reports that this variant causes reduced incorporation efficiency of a correct deoxyribonucleotide triphosphate (dNTP) in vitro (e.gSohl_2013). The following publications have been ascertained in the context of this evaluation (PMID: 12707443, 23208208, 21880868). ClinVar contains an entry for this variant (Variation ID: 206556). While this variant has been observed in individuals affected with autosomal dominant progressive external ophthalmoplegia, the clinical significance of the variant in this condition is currently unclear. Based on the evidence outlined above, this variant is pathogenic for autosomal recessive POLG-related disorders.

The p.Arg1096Cys variant in POLG gene has been previously reported many times with autosomal recessive inheritance pattern. Homozygous mutation of this variant was reported in a Saudi child with Alpers-Huttenlocher syndrome (AHS) (Kentab, 2019). Other reports could be accessed in The POLG Pathogenicity Prediction Server (http://polg.bmb.msu.edu).

The POLG c.3286C>T variant is predicted to result in the amino acid substitution p.Arg1096Cys. This variant has been reported to be causative for autosomal recessive POLG-associated disorders such as sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO), progressive external ophthalmoplegia (PEO) and sensory neuropathy, and Alpers’ Syndrome (Kurt et al. 2012. PMID: 24265579; Lax et al. 2012. PMID: 22189570; Ashley et al. 2008. PMID: 18487244; Hikmat et al. 2017. PubMed ID: 28471437). At least one heterozygous carrier of this particular variant presented with sporadic PEO (Agostino et al. 2003. PMID: 12707443). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/15-89861968-G-A). This variant is interpreted as pathogenic.