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

Clinical significance:Likely pathogenic (Last evaluated: Feb 25, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001293360.1

Allele description [Variation Report for NM_000199.5(SGSH):c.416C>T (p.Thr139Met)]

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

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.416C>T (p.Thr139Met)
HGVS:
  • NC_000017.11:g.80214705G>A
  • NG_008229.1:g.10696C>T
  • NM_000199.5:c.416C>TMANE SELECT
  • NM_000199.5:c.416C>TMANE SELECT
  • NM_001352921.3:c.416C>T
  • NM_001352922.2:c.416C>T
  • NP_000190.1:p.Thr139Met
  • NP_000190.1:p.Thr139Met
  • NP_001339850.1:p.Thr139Met
  • NP_001339851.1:p.Thr139Met
  • NC_000017.10:g.78188504G>A
  • NM_000199.3:c.416C>T
  • NR_148201.2:n.330C>T
Protein change:
T139M
Links:
dbSNP: rs775112689
NCBI 1000 Genomes Browser:
rs775112689
Molecular consequence:
  • NM_000199.5:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352921.3:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352922.2:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148201.2:n.330C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Intellectual disability
Synonyms:
Dull intelligence; Low intelligence; Mental deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0001071; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001481815Institute of Human Genetics, University of Leipzig Medical Centercriteria provided, single submitter
Likely pathogenic
(Feb 25, 2021)
unknownclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001481815.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testing PubMed (1)

Description

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 and classified as Likely Pathogenic (criteria: PM2_Supporting, PM3_Strong, PP3_Supporting, PP4_Supporting). This variant was identified in a compound heterozygous state with the variantNM_000199.5(SGSH):c.267C>A (p.Tyr89Ter) ( Variation ID: 983123).

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

Last Updated: Oct 24, 2021

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