ClinVar Miner

Submissions for variant NM_152419.3(HGSNAT):c.1464+1G>A

gnomAD frequency: 0.00001  dbSNP: rs398124545
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000082654 SCV000114696 pathogenic not provided 2013-06-18 criteria provided, single submitter clinical testing
Counsyl RCV000671662 SCV000796657 likely pathogenic Mucopolysaccharidosis, MPS-III-C 2017-12-21 criteria provided, single submitter clinical testing
Invitae RCV001221115 SCV001393139 pathogenic Mucopolysaccharidosis, MPS-III-C; Retinitis pigmentosa 73 2023-09-19 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 14 of the HGSNAT gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in HGSNAT are known to be pathogenic (PMID: 17033958, 19479962). This variant is present in population databases (rs398124545, gnomAD 0.002%). Disruption of this splice site has been observed in individuals with mucopolysaccharidosis type IIIC (PMID: 17397050, 28981474). ClinVar contains an entry for this variant (Variation ID: 96502). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000082654 SCV002061135 likely pathogenic not provided 2021-12-03 criteria provided, single submitter clinical testing Reported with another HGSNAT variant in a patient with retinitis pigmentosa in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Comander et al., 2017); Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 28981474, 17397050, 34047372)
Fulgent Genetics, Fulgent Genetics RCV001221115 SCV002813896 likely pathogenic Mucopolysaccharidosis, MPS-III-C; Retinitis pigmentosa 73 2022-01-11 criteria provided, single submitter clinical testing
Natera, Inc. RCV000671662 SCV002083317 pathogenic Mucopolysaccharidosis, MPS-III-C 2021-06-24 no assertion criteria provided clinical testing

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