NM_152419.3(HGSNAT):c.1250+1G>A AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: Oct 31, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001065437.2

Allele description [Variation Report for NM_152419.3(HGSNAT):c.1250+1G>A]

NM_152419.3(HGSNAT):c.1250+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.1250+1G>A
HGVS:
  • NC_000008.11:g.43191596G>A
  • NG_009552.1:g.56148G>A
  • NM_001363227.2:c.1250+1G>A
  • NM_001363228.2:c.1058+1G>A
  • NM_001363229.2:c.386+1G>A
  • NM_152419.3:c.1250+1G>AMANE SELECT
  • NC_000008.10:g.43046739G>A
  • NM_152419.2:c.1250+1G>A
Links:
dbSNP: rs398124544
NCBI 1000 Genomes Browser:
rs398124544
Molecular consequence:
  • NM_001363227.2:c.1250+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001363228.2:c.1058+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001363229.2:c.386+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_152419.3:c.1250+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV001230395Invitaecriteria provided, single submitter
Pathogenic
(Oct 31, 2020)
germlineclinical testing

PubMed (5)
[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

Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders.

Fernández-Marmiesse A, Morey M, Pineda M, Eiris J, Couce ML, Castro-Gago M, Fraga JM, Lacerda L, Gouveia S, Pérez-Poyato MS, Armstrong J, Castiñeiras D, Cocho JA.

Orphanet J Rare Dis. 2014 Apr 25;9:59. doi: 10.1186/1750-1172-9-59.

PubMed [citation]
PMID:
24767253
PMCID:
PMC4024120

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001230395.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change affects a donor splice site in intron 12 of the HGSNAT gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs398124544, ExAC 0.001%). This variant has been observed in individual(s) with autosomal recessive mucopolysaccharidosis type III (PMID: 17033958, 24767253). ClinVar contains an entry for this variant (Variation ID: 96500). This variant has also been reported as c.1334+1G>A. 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: Aug 27, 2021

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