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NM_000199.5(SGSH):c.416C>T (p.Thr139Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 25, 2021)
Last evaluated:
Feb 25, 2021
Accession:
VCV000551670.4
Variation ID:
551670
Description:
single nucleotide variant
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NM_000199.5(SGSH):c.416C>T (p.Thr139Met)

Allele ID
548468
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80214705 (GRCh38) GRCh38 UCSC
17: 78188504 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78188504G>A
NC_000017.11:g.80214705G>A
NM_000199.5:c.416C>T MANE Select NP_000190.1:p.Thr139Met missense
... more HGVS
Protein change
T139M
Other names
-
Canonical SPDI
NC_000017.11:80214704:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00001
Links
dbSNP: rs775112689
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, single submitter May 4, 2017 RCV000666794.2
Likely pathogenic 1 criteria provided, single submitter Feb 25, 2021 RCV001293360.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SGSH - - GRCh38
GRCh37
410 636

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 04, 2017)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-III-A
Allele origin: unknown
Counsyl
Accession: SCV000791150.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Likely pathogenic
(Feb 25, 2021)
criteria provided, single submitter
Method: clinical testing
Intellectual disability
(Autosomal recessive inheritance)
Allele origin: unknown
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001481815.1
Submitted: (Feb 25, 2021)
Evidence details
Comment:
The variant chr17-78188504-G-A, SGSH(NM_000199.5):c.416C>T,p.(Thr139Met) was identified in an individual with NDD. Inheritance was not applicable (heterozygous). The variant was reviewed according to current ACMG recommendations … (more)
Pathogenic
(Aug 01, 2019)
no assertion criteria provided
Method: research
Mucopolysaccharidosis, MPS-III-A
Allele origin: germline
Section for Clinical Neurogenetics,University of Tübingen
Accession: SCV001156105.1
Submitted: (Nov 26, 2019)
Evidence details
Publications
PubMed (2)

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
First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery. Hengel H European journal of human genetics : EJHG 2020 PMID: 32214227
Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA. Sidhu NS Acta crystallographica. Section D, Biological crystallography 2014 PMID: 24816101
Sanfilippo type A: new clinical manifestations and neuro-imaging findings in patients from the same family in Israel: a case report. Sharkia R Journal of medical case reports 2014 PMID: 24576347
Novel mutations in Sanfilippo A syndrome: implications for enzyme function. Weber B Human molecular genetics 1997 PMID: 9285796

Text-mined citations for rs775112689...

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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 Aug 27, 2021