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NM_152419.3(HGSNAT):c.1567A>C (p.Lys523Gln)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Nov 16, 2021)
Last evaluated:
Oct 11, 2021
Accession:
VCV000363150.9
Variation ID:
363150
Description:
single nucleotide variant
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NM_152419.3(HGSNAT):c.1567A>C (p.Lys523Gln)

Allele ID
314601
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p11.21
Genomic location
8: 43197696 (GRCh38) GRCh38 UCSC
8: 43052839 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.43052839A>C
NC_000008.11:g.43197696A>C
NG_009552.1:g.62248A>C
... more HGVS
Protein change
K523Q, K459Q, K235Q, K552Q
Other names
-
Canonical SPDI
NC_000008.11:43197695:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.04054 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.03393
Exome Aggregation Consortium (ExAC) 0.01063
Trans-Omics for Precision Medicine (TOPMed) 0.03632
Trans-Omics for Precision Medicine (TOPMed) 0.03718
The Genome Aggregation Database (gnomAD), exomes 0.00856
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03550
The Genome Aggregation Database (gnomAD) 0.03631
1000 Genomes Project 0.04054
Links
ClinGen: CA4736955
dbSNP: rs73569592
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Oct 11, 2021 RCV000592259.3
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000534224.3
Likely benign 2 criteria provided, single submitter Apr 27, 2017 RCV000398564.3
Benign 3 criteria provided, single submitter Jul 31, 2018 RCV000675865.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HGSNAT - - GRCh38
GRCh37
533 594

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-III-C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000474017.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (5)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Jan 05, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000700339.2
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa 73
Mucopolysaccharidosis, MPS-III-C
Allele origin: germline
Invitae
Accession: SCV000656047.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001886752.1
Submitted: (Sep 17, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 17033958, 21228398, 19823584, 20981092, 19479962, 20583299)
Likely benign
(Oct 11, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002014885.1
Submitted: (Nov 16, 2021)
Evidence details
Benign
(Sep 21, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801589.1
Submitted: (May 23, 2018)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Mucopolysaccharidosis type IIIC
Allele origin: germline
Natera, Inc.
Accession: SCV001460472.1
Submitted: (Dec 28, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001797490.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923003.1
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Functional analysis of the HGSNAT gene in patients with mucopolysaccharidosis IIIC (Sanfilippo C Syndrome). Fedele AO Human mutation 2010 PMID: 20583299
Protein misfolding as an underlying molecular defect in mucopolysaccharidosis III type C. Feldhammer M PloS one 2009 PMID: 19823584
Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: alpha-glucosaminide N-acetyltransferase (HGSNAT) gene. Feldhammer M Human mutation 2009 PMID: 19479962
Mutational analysis of the HGSNAT gene in Italian patients with mucopolysaccharidosis IIIC (Sanfilippo C syndrome). Mutation in brief #959. Online. Fedele AO Human mutation 2007 PMID: 17397050
Mutations in TMEM76* cause mucopolysaccharidosis IIIC (Sanfilippo C syndrome). Hrebícek M American journal of human genetics 2006 PMID: 17033958
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HGSNAT - - - -

Text-mined citations for rs73569592...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021