ClinVar Miner

Submissions for variant NM_018109.4(MTPAP):c.1432A>G (p.Asn478Asp)

gnomAD frequency: 0.00001  dbSNP: rs267606900
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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 RCV002513130 SCV003441423 pathogenic not provided 2024-03-09 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 478 of the MTPAP protein (p.Asn478Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with spastic ataxia (PMID: 20970105, 24651433). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 18391). 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 MTPAP protein function with a negative predictive value of 80%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000000002 SCV000020145 pathogenic Spastic ataxia 4 2014-12-01 no assertion criteria provided literature only

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