ClinVar Miner

Submissions for variant NM_001905.4(CTPS1):c.1769A>G (p.His590Arg)

gnomAD frequency: 0.00003  dbSNP: rs755468825
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001302682 SCV001491900 uncertain significance Severe combined immunodeficiency due to CTPS1 deficiency 2022-07-24 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 590 of the CTPS1 protein (p.His590Arg). This variant is present in population databases (rs755468825, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CTPS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1005750). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV004036248 SCV003755438 uncertain significance not specified 2021-09-16 criteria provided, single submitter clinical testing The c.1769A>G (p.H590R) alteration is located in exon 18 (coding exon 17) of the CTPS1 gene. This alteration results from a A to G substitution at nucleotide position 1769, causing the histidine (H) at amino acid position 590 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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