NM_152419.3(HGSNAT):c.852-1G>A AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: Feb 23, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001383039.1

Allele description [Variation Report for NM_152419.3(HGSNAT):c.852-1G>A]

NM_152419.3(HGSNAT):c.852-1G>A

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.852-1G>A
HGVS:
  • NC_000008.11:g.43178073G>A
  • NG_009552.1:g.42625G>A
  • NM_001363227.2:c.852-1G>A
  • NM_001363228.2:c.821-4072G>A
  • NM_001363229.2:c.-13-1G>A
  • NM_152419.3:c.852-1G>AMANE SELECT
  • NC_000008.10:g.43033216G>A
  • NM_152419.2:c.852-1G>A
Links:
dbSNP: rs1447092074
NCBI 1000 Genomes Browser:
rs1447092074
Molecular consequence:
  • NM_001363228.2:c.821-4072G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363227.2:c.852-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001363229.2:c.-13-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_152419.3:c.852-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001582048Invitaecriteria provided, single submitter
Pathogenic
(Feb 23, 2020)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Mutational analysis of the HGSNAT gene in Italian patients with mucopolysaccharidosis IIIC (Sanfilippo C syndrome). Mutation in brief #959. Online.

Fedele AO, Filocamo M, Di Rocco M, Sersale G, L├╝bke T, di Natale P, Cosma MP, Ballabio A.

Hum Mutat. 2007 May;28(5):523.

PubMed [citation]
PMID:
17397050

Molecular diagnosis of patients affected by mucopolysaccharidosis: a multicenter study.

Zanetti A, D'Avanzo F, Rigon L, Rampazzo A, Concolino D, Barone R, Volpi N, Santoro L, Lualdi S, Bertola F, Scarpa M, Tomanin R.

Eur J Pediatr. 2019 May;178(5):739-753. doi: 10.1007/s00431-019-03341-8. Epub 2019 Feb 26.

PubMed [citation]
PMID:
30809705
PMCID:
PMC6459791
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001582048.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects an acceptor splice site in intron 9 of the HGSNAT gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with mucopolysaccharidosis (PMID: 17397050, 30809705). ClinVar contains an entry for this variant (Variation ID: 556501). 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. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in HGSNAT are known to be pathogenic (PMID: 17033958, 19479962). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

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