ClinVar Miner

Submissions for variant NM_000271.5(NPC1):c.1436G>A (p.Cys479Tyr)

gnomAD frequency: 0.00001  dbSNP: rs1555636659
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000649020 SCV000770841 pathogenic Niemann-Pick disease, type C1 2022-06-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. 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 expected to disrupt NPC1 protein function. ClinVar contains an entry for this variant (Variation ID: 539310). This missense change has been observed in individual(s) with Niemann-Pick disease (PMID: 16098014, 20718790; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 479 of the NPC1 protein (p.Cys479Tyr).
Eurofins Ntd Llc (ga) RCV000728564 SCV000856156 uncertain significance not provided 2017-08-10 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000649020 SCV000915802 uncertain significance Niemann-Pick disease, type C1 2018-11-15 criteria provided, single submitter clinical testing The NPC1 c.1436G>A (p.Cys479Tyr) missense variant has been reported in two studies and is found in two individuals with Niemann-Pick disease type C, including one each in a compound heterozygous state with a second missense variant and in a heterozygous state (Fernandez-Valero et al. 2005; Macias-Vidal et al. 2011). The p.Cys479Tyr variant was absent from 100 controls and is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium or the Genome Aggregation Database. Based on the limited evidence, the p.Cys479Tyr variant is classified as a variant of unknown significance but suspicious for pathogenicity for Niemann-Pick disease type C. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Baylor Genetics RCV000649020 SCV001163439 likely pathogenic Niemann-Pick disease, type C1 criteria provided, single submitter clinical testing
Ambry Genetics RCV003243238 SCV003965413 likely pathogenic Inborn genetic diseases 2023-03-30 criteria provided, single submitter clinical testing The c.1436G>A (p.C479Y) alteration is located in coding exon 9 of the NPC1 gene. This alteration results from a G to A substitution at nucleotide position 1436, causing the cysteine (C) at amino acid position 479 to be replaced by a tyrosine (Y). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been detected in a Spanish child who developed generalized seizures at age 9 and was later diagnosed with Niemann-Pick disease type C at age 11. The child was heterozygous for this variant and a second mutation was not able to be detected (Fernandez-Valero 2005; Macías-Vidal 2011). This variant was also reported in trans with a second NPC1 mutation (p.A1054T c.3160G>A) in another Spanish child with severe infantile onset (Macías-Vidal 2011). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.
Natera, Inc. RCV000649020 SCV001455874 uncertain significance Niemann-Pick disease, type C1 2020-09-16 no assertion criteria provided clinical testing

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