NM_000199.5(SGSH):c.98G>A (p.Gly33Glu) AND Mucopolysaccharidosis, MPS-III-A

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 2022
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:: RCV002005530.4

Allele description [Variation Report for NM_000199.5(SGSH):c.98G>A (p.Gly33Glu)]

NM_000199.5(SGSH):c.98G>A (p.Gly33Glu)

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.98G>A (p.Gly33Glu)

HGVS:

NC_000017.11:g.80217183C>T
NG_008229.1:g.8218G>A
NM_000199.5:c.98G>AMANE SELECT
NM_001352921.3:c.98G>A
NM_001352922.2:c.98G>A
NP_000190.1:p.Gly33Glu
NP_001339850.1:p.Gly33Glu
NP_001339851.1:p.Gly33Glu
NC_000017.10:g.78190982C>T
NR_148201.2:n.118G>A

Protein change:

G33E

Links:

dbSNP: rs762732038

NCBI 1000 Genomes Browser:

rs762732038

Molecular consequence:

NM_000199.5:c.98G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352921.3:c.98G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352922.2:c.98G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148201.2:n.118G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Mucopolysaccharidosis, MPS-III-A (MPS3A)
Synonyms:: SULFAMIDASE DEFICIENCY; Mucopoly-saccharidosis type 3A; Sanfilippo syndrome A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009655; MedGen: C0086647; Orphanet: 581; Orphanet: 79269; OMIM: 252900

Recent activity

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RASL10B RAS like family 10 member B [Homo sapiens]
RASL10B RAS like family 10 member B [Homo sapiens]
Gene ID:91608

Gene
Gene Links for GEO Profiles (Select 81655507) (1)
Gene
Homologene neighbors for GEO Profiles (Select 81642016) (0)
GEO Profiles
Homo sapiens chromosome 6 genomic scaffold, GRCh38.p14 alternate locus group ALT...
Homo sapiens chromosome 6 genomic scaffold, GRCh38.p14 alternate locus group ALT_REF_LOCI_3 HSCHR6_MHC_DBB_CTG1
gi|568815551|gnl|ASM:GCF_000001335. HR6_MHC_DBB_CTG1|ref|NT_167245.2||gpp|GPS_003206087.1|

Nucleotide
Profile neighbors for GEO Profiles (Select 81648901) (199)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002269178	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002269178

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002269178.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with SGSH-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SGSH protein function. ClinVar contains an entry for this variant (Variation ID: 1484078). This variant is present in population databases (rs762732038, gnomAD 0.004%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 33 of the SGSH protein (p.Gly33Glu).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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