NM_152419.3(HGSNAT):c.7G>C (p.Gly3Arg) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Sep 23, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_152419.3(HGSNAT):c.7G>C (p.Gly3Arg)]

NM_152419.3(HGSNAT):c.7G>C (p.Gly3Arg)

HGSNAT:heparan-alpha-glucosaminide N-acetyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_152419.3(HGSNAT):c.7G>C (p.Gly3Arg)
  • NC_000008.11:g.43140503G>C
  • NG_009552.1:g.5055G>C
  • NM_001363227.2:c.7G>C
  • NM_001363228.2:c.7G>C
  • NM_001363229.2:c.-827G>C
  • NM_152419.3:c.7G>CMANE SELECT
  • NP_001350156.1:p.Gly3Arg
  • NP_001350157.1:p.Gly3Arg
  • NP_689632.2:p.Gly3Arg
  • NC_000008.10:g.42995646G>C
Protein change:
dbSNP: rs1387365931
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001363229.2:c.-827G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363227.2:c.7G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363228.2:c.7G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152419.3:c.7G>C - missense variant - [Sequence Ontology: SO:0001583]


Mucopolysaccharidosis, MPS-III-C (MPS3C)
Mucopoly-saccharidosis type 3C; Sanfilippo syndrome C; Acetyl-CoA alpha-glucosaminide n-acetyltransferase deficiency; See all synonyms [MedGen]
MONDO: MONDO:0009657; MedGen: C0086649; Orphanet: 581; Orphanet: 79271; OMIM: 252930
Retinitis pigmentosa 73 (RP73)
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)
SCV001538439Invitaecriteria provided, single submitter
Uncertain significance
(Sep 23, 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



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]

Details of each submission

From Invitae, SCV001538439.1

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


This sequence change replaces glycine with arginine at codon 3 of the HGSNAT protein (p.Gly3Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: Deleterious; PolyPhen-2: Not Available; Align-GVGD: Class C0. The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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

Last Updated: Nov 27, 2021

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