Submissions for variant NM_001363711.2(DUOX2):c.1462G>A (p.Gly488Arg)

gnomAD frequency: 0.00024  dbSNP: rs191759494

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	RCV000490324	SCV000267295	likely pathogenic	Thyroid dyshormonogenesis 6	2016-03-18	criteria provided, single submitter	reference population
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000614180	SCV000731474	pathogenic	Familial thyroid dyshormonogenesis	2017-04-14	criteria provided, single submitter	clinical testing	The p.Gly488Arg (NM014080.4 c.1462G>A) variant in DUOX2 has been reported in 9 h eterozygous, 3 homozygous, and 8 compound heterozygous Asian individuals with cl inical features of congenital hypothyroidism and related disorders (Narumi 2011, Yoshizawa-Ogasawara 2013, Jin 2014, Park 2016, Srichomkwun 2017). This variant has been identified in 0.15% (13/8,652) of East Asian chromosomes by the Exome A ggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs191759494). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro func tional studies provide support that the p.Gly488Arg variant impacts protein func tion (Narumi 2011 and Jin 2015). In summary, this variant meets criteria to be c lassified as pathogenic for congenital hypothyroidism and related disorders in a n autosomal recessive manner based upon biallelic occurrence in affected individ uals, low frequency in control populations, and functional studies.
Illumina Laboratory Services, Illumina	RCV000490324	SCV000915683	pathogenic	Thyroid dyshormonogenesis 6	2018-08-15	criteria provided, single submitter	clinical testing	Across a selection of the available literature, the DUOX2 c.1462G>A (p.Gly488Arg) missense variant has been reported in at least 18 unrelated patients with congenital hypothyroidism, including in a homozygous state in two siblings and an unrelated individual, in a compound heterozygous state in at least seven individuals, and in a heterozygous state in nine individuals in whom a second variant in the DUOX2 gene was not identified (Narumi et al. 2011; Yoshizawa-Ogasawara et al. 2013; Jin et al. 2014; Park et al. 2016; Srichomkwun et al. 2017). In several of these cases, the variant was shown to be inherited from an unaffected parent. In addition, one patient with dyshormonogenesis and an enlarged thyroid was heterozygous for the p.Gly488Arg variant and a second missense variant, but phase was not specified (Narumi et al. 2011). The p.Gly488Arg variant was absent from at least 100 alleles and is reported at a frequency of 0.001503 in the East Asian population of the Exome Aggregation Consortium. By assaying hydrogen peroxide production, two independent groups showed the variant protein displays greatly reduced activity compared to the wild type protein in HEK293 and A549 cells (Narumi et al. 2011; Jin et al. 2014). Based on the collective evidence, the p.Gly488Arg variant is classified as pathogenic for congenital hypothyroidism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
GeneDx	RCV001582720	SCV001811087	pathogenic	not provided	2023-08-02	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect as the generation of H2O2 was significantly reduced in the G488R transfected cells (PMID: 25248169, 21900383); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27821020, 34200080, 31044655, 21900383, 26709262, 25248169, 30609409, 29650690, 32469330, 32459320, 29092890, 23457309, 32425884, 34426522, 33631011, 33651715)
3billion	RCV000490324	SCV002521071	pathogenic	Thyroid dyshormonogenesis 6	2022-05-22	criteria provided, single submitter	clinical testing	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.015%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.71; 3Cnet: 0.51). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000225342). 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: 21900383, 23457309, 25248169, 26709262). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Fulgent Genetics, Fulgent Genetics	RCV000490324	SCV002808640	pathogenic	Thyroid dyshormonogenesis 6	2022-02-26	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002515593	SCV003741498	likely pathogenic	Inborn genetic diseases	2021-02-24	criteria provided, single submitter	clinical testing	The c.1462G>A (p.G488R) alteration is located in exon 13 (coding exon 12) of the DUOX2 gene. This alteration results from a G to A substitution at nucleotide position 1462, causing the glycine (G) at amino acid position 488 to be replaced by an arginine (R). Based on data from the Genome Aggregation Database (gnomAD) database, the DUOX2 c.1462G>A alteration was observed in 0.015% (42/282816) of total alleles studied, with a frequency of 0.12% (24/19952) in the East Asian subpopulation. This alteration has been detected in multiple individuals with congenital hypothyroidism, in the homozygous state, the compound heterozygous state, and in the heterozygous state without a second alteration identified (Narumi, 2011; Yoshizawa-Ogasawara, 2013; Jin, 2014; Srichomkwun, 2017; Sun, 2018; Abe, 2018; Peters, 2019). This amino acid position is highly conserved in available vertebrate species. A hydrogen peroxide production assay showed significantly decreased hydrogen peroxide compared to wild type protein in HEK293 and A549 cells (Narumi, 2011; Jin, 2014). The in silico prediction for the p.G488R alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic.
PreventionGenetics, part of Exact Sciences	RCV003417764	SCV004114397	pathogenic	DUOX2-related condition	2023-09-01	criteria provided, single submitter	clinical testing	The DUOX2 c.1462G>A variant is predicted to result in the amino acid substitution p.Gly488Arg. This variant was reported in individuals with autosomal recessive congenital hypothyroidism and thyroid dyshormonogenesis, with complete loss of function observed in functional in vitro assays (Narumi et al. 2011. PubMed ID: 21900383; Yoshizawa-Ogasawara et al. 2013. PubMed ID: 23457309; Jin et al. 2014. PubMed ID: 25248169). This variant is reported in 0.12% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/15-45400357-C-T) and is reported as likely pathogenic or pathogenic by many outside laboratories in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/225342/). This variant is interpreted as pathogenic.
University of Washington Center for Mendelian Genomics, University of Washington	RCV000755103	SCV000882921	likely pathogenic	Nongoitrous Euthyroid Hyperthyrotropinemia	2017-01-01	no assertion criteria provided	research