NM_152419.3(HGSNAT):c.98C>T (p.Ala33Val) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Jul 20, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001351299.1

Allele description [Variation Report for NM_152419.3(HGSNAT):c.98C>T (p.Ala33Val)]

NM_152419.3(HGSNAT):c.98C>T (p.Ala33Val)

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.98C>T (p.Ala33Val)
HGVS:
  • NC_000008.11:g.43140594C>T
  • NG_009552.1:g.5146C>T
  • NM_001363227.2:c.98C>T
  • NM_001363228.2:c.98C>T
  • NM_001363229.2:c.-736C>T
  • NM_152419.3:c.98C>TMANE SELECT
  • NP_001350156.1:p.Ala33Val
  • NP_001350157.1:p.Ala33Val
  • NP_689632.2:p.Ala33Val
  • NC_000008.10:g.42995737C>T
Protein change:
A33V
Links:
dbSNP: rs1802483575
NCBI 1000 Genomes Browser:
rs1802483575
Molecular consequence:
  • NM_001363229.2:c.-736C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363227.2:c.98C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363228.2:c.98C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152419.3:c.98C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001545751Invitaecriteria provided, single submitter
Uncertain significance
(Jul 20, 2020)
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, SCV001545751.1

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

Description

This sequence change replaces alanine with valine at codon 33 of the HGSNAT protein (p.Ala33Val). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and valine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with HGSNAT-related conditions. 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 HGSNAT protein function. 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: Nov 27, 2021

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