Submissions for variant NM_000030.3(AGXT):c.836T>C (p.Ile279Thr)

gnomAD frequency: 0.00171  dbSNP: rs140992177

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000180093	SCV000232462	benign	not specified	2015-04-15	criteria provided, single submitter	clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory	RCV000186256	SCV000239580	uncertain significance	Primary hyperoxaluria, type I	2023-12-23	criteria provided, single submitter	clinical testing	This variant has been confirmed to be pathogenic in vivo when expressed on the background of the minor allele (AGXT c.32C>T)(PMID:19479957) but, when expressed on the major allele (AGXT c.32C=), it has normal activity in vitro (PID:15963748). Interpretation therefore requires knowledge of the haplotype. ACMG for expression on minor allele:PS3 PM2 PM3 PP3 PP4 BP6 (Pathogenic) ACMG for expression on major allele:PM2 PP3 BS3 BP2 BP6 (likely benign)
Invitae	RCV000966394	SCV001113712	likely benign	not provided	2024-01-31	criteria provided, single submitter	clinical testing
Mendelics	RCV000186256	SCV001136275	benign	Primary hyperoxaluria, type I	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000186256	SCV001297134	likely benign	Primary hyperoxaluria, type I	2017-08-25	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000180093	SCV002548355	likely benign	not specified	2022-05-11	criteria provided, single submitter	clinical testing	Variant summary: AGXT c.836T>C (p.Ile279Thr) results in a non-conservative amino acid change located in the Aminotransferase class V domain (IPR000192) 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 0.0018 in 251244 control chromosomes, predominantly at a frequency of 0.003 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately equal to the estimated maximal expected allele frequency for a pathogenic variant in AGXT causing Primary Hyperoxaluria Type 1 phenotype (0.0024), suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.836T>C has been reported in the literature in individuals affected with Primary Hyperoxaluria Type 1 without strong evidence of causality (e.g. Coulter-Mackie_2005, Monico_2007, Hoyer-Kuhn_2014, Mandrile_2014, Hopp_2015). Importantly, co-occurrences of the variant in cis with known pathogenic variants in at least 5 compound heterozygous individuals have been reported (Coulter-Mackie_2005, Monico_2007), providing supporting evidence for a benign role. Experimental evidence evaluating an impact on protein function demonstrated the variant has essentially normal enzymatic activity (Coulter-Mackie_2005). Five ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
Fulgent Genetics, Fulgent Genetics	RCV000186256	SCV002804296	likely benign	Primary hyperoxaluria, type I	2021-07-08	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003937630	SCV004748555	likely benign	AGXT-related condition	2021-02-17	criteria provided, single submitter	clinical testing	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).
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000966394	SCV001549730	likely benign	not provided		no assertion criteria provided	clinical testing	The AGXT p.Ile279Thr variant was identified in the literature in 4/55 probands with type 1 primary hyperoxaluria, however in three of these probands already carried two presumed pathogenic variants (Monico_2007_PMID:17460142). The variant was also found in two other cases of type 1 primary hyperoxaluria but was found on the same allele as the c.33_34ins variant (Coulter-Mackie_2005_PMID:15963748). The variant was identified in dbSNP (ID: rs140992177), ClinVar (classified as benign by EGL Genetic Diagnostics and as uncertain significance by Clinical Biochemistry Laboratory, Health Services Laboratory) and LOVD 3.0 (classified as likely pathogenic). The variant was identified in control databases in 510 of 282628 chromosomes at a frequency of 0.001804 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 380 of 129022 chromosomes (freq: 0.002945), South Asian in 71 of 30608 chromosomes (freq: 0.00232), Other in 11 of 7222 chromosomes (freq: 0.001523), European (Finnish) in 16 of 25118 chromosomes (freq: 0.000637), Latino in 16 of 35412 chromosomes (freq: 0.000452), African in 11 of 24942 chromosomes (freq: 0.000441), Ashkenazi Jewish in 3 of 10360 chromosomes (freq: 0.00029), and East Asian in 2 of 19944 chromosomes (freq: 0.0001). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Ile279 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. Functional analysis of alanine:glyoxylate aminotransferase activity was not found to be affected with the p.I279T variant. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Natera, Inc.	RCV000186256	SCV002076479	likely benign	Primary hyperoxaluria, type I	2020-04-25	no assertion criteria provided	clinical testing