ClinVar Miner

Submissions for variant NM_000489.6(ATRX):c.1825C>G (p.Pro609Ala)

gnomAD frequency: 0.00024  dbSNP: rs186742436
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000861727 SCV001002119 benign Alpha thalassemia-X-linked intellectual disability syndrome 2024-01-30 criteria provided, single submitter clinical testing
GeneDx RCV001594847 SCV001828160 benign not provided 2020-10-27 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 30359267)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000120182 SCV002548050 benign not specified 2022-05-11 criteria provided, single submitter clinical testing Variant summary: ATRX c.1825C>G (p.Pro609Ala) 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 0.0011 in 183133 control chromosomes, predominantly at a frequency of 0.014 within the East Asian subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in ATRX causing ATR-X Syndrome phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. To our knowledge, no experimental evidence demonstrating its impact on protein function have been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as benign (n=2) and likely benign (n=1). Based on the evidence outlined above, the variant was classified as benign.
ITMI RCV000120182 SCV000084326 not provided not specified 2013-09-19 no assertion provided reference population
Natera, Inc. RCV000861727 SCV001458091 likely benign Alpha thalassemia-X-linked intellectual disability syndrome 2020-01-07 no assertion criteria provided clinical testing

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