ClinVar Miner

Submissions for variant NM_004722.4(AP4M1):c.1100G>A (p.Arg367Gln)

gnomAD frequency: 0.00021  dbSNP: rs139861201
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000433329 SCV000528693 uncertain significance not provided 2024-02-06 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 32979048)
Fulgent Genetics, Fulgent Genetics RCV000765979 SCV000897402 uncertain significance Hereditary spastic paraplegia 50 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000765979 SCV000957339 uncertain significance Hereditary spastic paraplegia 50 2024-01-25 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 367 of the AP4M1 protein (p.Arg367Gln). This variant is present in population databases (rs139861201, gnomAD 0.05%). This missense change has been observed in individual(s) with hereditary spastic paraplegia (PMID: 32979048). ClinVar contains an entry for this variant (Variation ID: 386884). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt AP4M1 protein function with a negative predictive value of 80%. 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.
CeGaT Center for Human Genetics Tuebingen RCV000433329 SCV002062764 uncertain significance not provided 2021-12-01 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001848781 SCV002105673 uncertain significance Hereditary spastic paraplegia 2021-11-15 criteria provided, single submitter clinical testing
Yale Center for Mendelian Genomics, Yale University RCV001849371 SCV002106881 likely pathogenic Spastic paraplegia 2020-10-01 no assertion criteria provided literature only

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