NM_152419.3(HGSNAT):c.1128G>A (p.Ser376=) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Aug 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001241541.1

Allele description [Variation Report for NM_152419.3(HGSNAT):c.1128G>A (p.Ser376=)]

NM_152419.3(HGSNAT):c.1128G>A (p.Ser376=)

Gene:
HGSNAT:heparan-alpha-glucosaminide N-acetyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p11.21
Genomic location:
Preferred name:
NM_152419.3(HGSNAT):c.1128G>A (p.Ser376=)
HGVS:
  • NC_000008.11:g.43182260G>A
  • NG_009552.1:g.46812G>A
  • NM_001363227.2:c.1128G>A
  • NM_001363228.2:c.936G>A
  • NM_001363229.2:c.264G>A
  • NM_152419.3:c.1128G>AMANE SELECT
  • NP_001350156.1:p.Ser376=
  • NP_001350157.1:p.Ser312=
  • NP_001350158.1:p.Ser88=
  • NP_689632.2:p.Ser376=
  • NC_000008.10:g.43037403G>A
  • NM_152419.2:c.1128G>A
Links:
dbSNP: rs770462636
NCBI 1000 Genomes Browser:
rs770462636
Molecular consequence:
  • NM_001363227.2:c.1128G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363228.2:c.936G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363229.2:c.264G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_152419.3:c.1128G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Mucopolysaccharidosis, MPS-III-C (MPS3C)
Synonyms:
Mucopoly-saccharidosis type 3C; Sanfilippo syndrome C; Acetyl-CoA alpha-glucosaminide n-acetyltransferase deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009657; MedGen: C0086649; Orphanet: 581; Orphanet: 79271; OMIM: 252930
Name:
Retinitis pigmentosa 73 (RP73)
Identifiers:
MONDO: MONDO:0014687; MedGen: C4225287; Orphanet: 791; OMIM: 616544

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001414564Invitaecriteria provided, single submitter
Uncertain significance
(Aug 28, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001414564.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change affects codon 376 of the HGSNAT mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the HGSNAT protein. This variant also falls at the last nucleotide of exon 11 of the HGSNAT coding sequence, which is part of the consensus splice site for this exon. This variant is present in population databases (rs770462636, ExAC 0.001%). This variant has not been reported in the literature in individuals with HGSNAT-related conditions. ClinVar contains an entry for this variant (Variation ID: 363146). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 8, 2022

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