NM_152419.3(HGSNAT):c.1886A>G (p.Lys629Arg) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Jan 8, 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.1886A>G (p.Lys629Arg)]

NM_152419.3(HGSNAT):c.1886A>G (p.Lys629Arg)

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.1886A>G (p.Lys629Arg)
  • NC_000008.11:g.43199547A>G
  • NG_009552.1:g.64099A>G
  • NM_001363227.2:c.1973A>G
  • NM_001363228.2:c.1694A>G
  • NM_001363229.2:c.1022A>G
  • NM_152419.3:c.1886A>GMANE SELECT
  • NP_001350156.1:p.Lys658Arg
  • NP_001350157.1:p.Lys565Arg
  • NP_001350158.1:p.Lys341Arg
  • NP_689632.2:p.Lys629Arg
  • NC_000008.10:g.43054690A>G
  • NM_152419.2:c.1886A>G
Protein change:
dbSNP: rs1804852352
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001363227.2:c.1973A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363228.2:c.1694A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363229.2:c.1022A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152419.3:c.1886A>G - 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)
SCV001391944Invitaecriteria provided, single submitter
Uncertain significance
(Jan 8, 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, SCV001391944.2

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


This sequence change replaces lysine with arginine at codon 629 of the HGSNAT protein (p.Lys629Arg). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and arginine. This variant is not present in population databases (ExAC no frequency). 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a 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.

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

Last Updated: Nov 27, 2021

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