NM_152419.3(HGSNAT):c.940A>G (p.Ile314Val) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Oct 29, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001231200.2

Allele description [Variation Report for NM_152419.3(HGSNAT):c.940A>G (p.Ile314Val)]

NM_152419.3(HGSNAT):c.940A>G (p.Ile314Val)

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.940A>G (p.Ile314Val)
HGVS:
  • NC_000008.11:g.43178162A>G
  • NG_009552.1:g.42714A>G
  • NM_001363227.2:c.940A>G
  • NM_001363228.2:c.821-3983A>G
  • NM_001363229.2:c.76A>G
  • NM_152419.3:c.940A>GMANE SELECT
  • NP_001350156.1:p.Ile314Val
  • NP_001350158.1:p.Ile26Val
  • NP_689632.2:p.Ile314Val
  • NC_000008.10:g.43033305A>G
  • NM_152419.2:c.940A>G
Protein change:
I26V
Links:
dbSNP: rs1446334240
NCBI 1000 Genomes Browser:
rs1446334240
Molecular consequence:
  • NM_001363228.2:c.821-3983A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363227.2:c.940A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363229.2:c.76A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152419.3:c.940A>G - 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
SCV001403712Invitaecriteria provided, single submitter
Uncertain significance
(Oct 29, 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, SCV001403712.2

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

Description

This sequence change replaces isoleucine with valine at codon 314 of the HGSNAT protein (p.Ile314Val). The isoleucine residue is moderately conserved and there is a small physicochemical difference between isoleucine and valine. 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 output the following: SIFT: Tolerated; PolyPhen-2: Benign; Align-GVGD: Class C0. The valine 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.

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

Last Updated: Nov 27, 2021

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