15-45108159-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PP5_Very_Strong
The NM_001363711.2(DUOX2):c.1462G>A(p.Gly488Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001363711.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DUOX2 | ENST00000389039.11 | c.1462G>A | p.Gly488Arg | missense_variant | Exon 13 of 34 | 1 | NM_001363711.2 | ENSP00000373691.7 | ||
DUOX2 | ENST00000603300.1 | c.1462G>A | p.Gly488Arg | missense_variant | Exon 13 of 34 | 1 | ENSP00000475084.1 | |||
DUOX2 | ENST00000558383.1 | n.3193G>A | non_coding_transcript_exon_variant | Exon 7 of 17 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152160Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251434Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135904
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461854Hom.: 0 Cov.: 33 AF XY: 0.0000935 AC XY: 68AN XY: 727234
GnomAD4 genome AF: 0.000250 AC: 38AN: 152278Hom.: 0 Cov.: 30 AF XY: 0.000228 AC XY: 17AN XY: 74464
ClinVar
Submissions by phenotype
Thyroid dyshormonogenesis 6 Pathogenic:4
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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. -
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. -
Inborn genetic diseases Pathogenic:1
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. -
DUOX2-related disorder Pathogenic:1
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. -
not provided Pathogenic:1
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, 38373250, 34564849, 39029043) -
Nongoitrous Euthyroid Hyperthyrotropinemia Pathogenic:1
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Familial thyroid dyshormonogenesis Pathogenic:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at