ClinVar Miner

Submissions for variant NM_001368809.2(AMPD2):c.1859G>A (p.Arg620His)

gnomAD frequency: 0.00001  dbSNP: rs587777395
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000119282 SCV001519924 pathogenic Pontocerebellar hypoplasia type 9 2022-02-21 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002515805 SCV002979315 likely pathogenic Hereditary spastic paraplegia 63; Pontocerebellar hypoplasia type 9 2023-06-29 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies have shown that this missense change affects AMPD2 function (PMID: 23911318). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 674 of the AMPD2 protein (p.Arg674His). This variant is present in population databases (rs587777395, gnomAD 0.005%). This missense change has been observed in individuals with pontocerebellar hypoplasia (PMID: 23911318, 31130284). It has also been observed to segregate with disease in related individuals. This variant is also known as NM_203404.1:c.1664G>A (p.Arg555His). ClinVar contains an entry for this variant (Variation ID: 132813). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive.
Genome-Nilou Lab RCV003343648 SCV004050605 likely pathogenic Hereditary spastic paraplegia 63 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000119282 SCV004050606 likely pathogenic Pontocerebellar hypoplasia type 9 2023-04-11 criteria provided, single submitter clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV000119282 SCV004801197 pathogenic Pontocerebellar hypoplasia type 9 2024-03-14 criteria provided, single submitter research
OMIM RCV000119282 SCV000154717 pathogenic Pontocerebellar hypoplasia type 9 2013-08-01 no assertion criteria provided literature only

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