NM_000199.5(SGSH):c.1063G>A (p.Glu355Lys) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 3, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000414288.1

Allele description [Variation Report for NM_000199.5(SGSH):c.1063G>A (p.Glu355Lys)]

NM_000199.5(SGSH):c.1063G>A (p.Glu355Lys)

Gene:
SGSH:N-sulfoglucosamine sulfohydrolase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000199.5(SGSH):c.1063G>A (p.Glu355Lys)
HGVS:
  • NC_000017.11:g.80210898C>T
  • NG_008229.1:g.14503G>A
  • NG_032778.1:g.45907C>T
  • NM_000199.5:c.1063G>AMANE SELECT
  • NM_001352921.3:c.*150G>A
  • NM_001352922.2:c.*113G>A
  • NP_000190.1:p.Glu355Lys
  • LRG_1330:g.45907C>T
  • NC_000017.10:g.78184697C>T
  • NM_000199.3:c.1063G>A
  • NR_148201.2:n.977G>A
  • P51688:p.Glu355Lys
Protein change:
E355K
Links:
UniProtKB: P51688#VAR_054689; dbSNP: rs766938111
NCBI 1000 Genomes Browser:
rs766938111
Molecular consequence:
  • NM_001352921.3:c.*150G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001352922.2:c.*113G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000199.5:c.1063G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148201.2:n.977G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000491270GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 3, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000491270.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The E355K variant in the SGSH gene has been reported previously in association with autosomal recessive mucopolysaccharidosis type IIIA when present in trans with another disease-causing pathogenic variant (Beesley et al., 2000; Kousi et al., 2012). Structural analysis of SGSH using a crystal model predicted the E355K variant resulted in the loss of the surface salt bridge with Arg304 and of the hydrogen bonds to Ser309 and Glu310 (Sidhu et al., 2014). The E355K variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The E355K variant is a non-conservative amino acid substitution, which occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The E355K variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Nov 27, 2021

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