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NM_152419.3(HGSNAT):c.715C>T (p.Arg239Cys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 30, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003235516.1

Allele description [Variation Report for NM_152419.3(HGSNAT):c.715C>T (p.Arg239Cys)]

NM_152419.3(HGSNAT):c.715C>T (p.Arg239Cys)

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.715C>T (p.Arg239Cys)
HGVS:
  • NC_000008.11:g.43170666C>T
  • NG_009552.1:g.35218C>T
  • NM_001363227.2:c.715C>T
  • NM_001363228.2:c.715C>T
  • NM_001363229.2:c.-119C>T
  • NM_152419.3:c.715C>TMANE SELECT
  • NP_001350156.1:p.Arg239Cys
  • NP_001350157.1:p.Arg239Cys
  • NP_689632.2:p.Arg239Cys
  • NC_000008.10:g.43025809C>T
  • NC_000008.10:g.43025809C>T
  • NM_152419.2:c.715C>T
Protein change:
R239C
Links:
dbSNP: rs369292480
NCBI 1000 Genomes Browser:
rs369292480
Molecular consequence:
  • NM_001363229.2:c.-119C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363227.2:c.715C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363228.2:c.715C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152419.3:c.715C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003934211Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(May 30, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

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

Citations

PubMed

A genetic and clinical study of individuals with nonsyndromic retinopathy consequent upon sequence variants in HGSNAT, the gene associated with Sanfilippo C mucopolysaccharidosis.

Schiff ER, Daich Varela M, Robson AG, Pierpoint K, Ba-Abbad R, Nutan S, Zein WM, Ullah E, Huryn LA, Tuupanen S, Mahroo OA, Michaelides M, Burke D, Harvey K, Arno G, Hufnagel RB, Webster AR.

Am J Med Genet C Semin Med Genet. 2020 Sep;184(3):631-643. doi: 10.1002/ajmg.c.31822. Epub 2020 Aug 7.

PubMed [citation]
PMID:
32770643
PMCID:
PMC8125330

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934211.1

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

Description

Variant summary: HGSNAT c.715C>T (p.Arg239Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3e-05 in 235520 control chromosomes (gnomAD). c.715C>T has been reported in the literature in the homozygous state in an individual affected with non-syndromic Retinitis Pigmentosa (Schiff_2020). These data indicate that the variant may be associated with Retinitis Pigmentosa 73. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 32770643). Four submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as either VUS (n=2) or pathogenic (n=1)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

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

Last Updated: Sep 29, 2024