NM_000199.5(SGSH):c.1320C>A (p.Asp440Glu) AND Mucopolysaccharidosis, MPS-III-A

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 11, 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:: RCV002608415.1

Allele description

NM_000199.5(SGSH):c.1320C>A (p.Asp440Glu)

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.1320C>A (p.Asp440Glu)

HGVS:

NC_000017.11:g.80210641G>T
NG_008229.1:g.14760C>A
NG_008229.2:g.14692C>A
NG_032778.1:g.45650G>T
NM_000199.5:c.1320C>AMANE SELECT
NM_001352921.3:c.*407C>A
NM_001352922.2:c.*370C>A
NP_000190.1:p.Asp440Glu
LRG_1330:g.45650G>T
NC_000017.10:g.78184440G>T
NR_148201.2:n.1234C>A

Protein change:

D440E

Molecular consequence:

NM_001352921.3:c.*407C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001352922.2:c.*370C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000199.5:c.1320C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148201.2:n.1234C>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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Piptolepis oleaster voucher SPF:Loeuille et al. 517 NADH dehydrogenase (ndhF) ge...
Piptolepis oleaster voucher SPF:Loeuille et al. 517 NADH dehydrogenase (ndhF) gene, partial cds; chloroplast
gi|706072048|gb|KM278518.1|

Nucleotide
Paralychnophora bicolor x Paralychnophora patriciana voucher SPF:Loeuille et al....
Paralychnophora bicolor x Paralychnophora patriciana voucher SPF:Loeuille et al. 326 NADH dehydrogenase (ndhF) gene, partial cds; chloroplast
gi|706072046|gb|KM278517.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002956163	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 11, 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

SCV002956163

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 11, 2022)

germline

clinical testing

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

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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 Invitae, SCV002956163.1

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 440 of the SGSH protein (p.Asp440Glu). This variant is present in population databases (rs751683275, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SGSH-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

#	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: Feb 13, 2023

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