NM_000199.5(SGSH):c.1081G>A (p.Val361Ile) AND not provided

Clinical significance:Benign (Last evaluated: Aug 22, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000589061.2

Allele description [Variation Report for NM_000199.5(SGSH):c.1081G>A (p.Val361Ile)]

NM_000199.5(SGSH):c.1081G>A (p.Val361Ile)

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.1081G>A (p.Val361Ile)
HGVS:
  • NC_000017.11:g.80210880C>T
  • NG_008229.1:g.14521G>A
  • NG_032778.1:g.45889C>T
  • NM_000199.5:c.1081G>AMANE SELECT
  • NM_000199.5:c.1081G>AMANE SELECT
  • NM_001352921.3:c.*168G>A
  • NM_001352922.2:c.*131G>A
  • NP_000190.1:p.Val361Ile
  • NP_000190.1:p.Val361Ile
  • NP_000190.1:p.Val361Ile
  • LRG_1330:g.45889C>T
  • NC_000017.10:g.78184679C>T
  • NC_000017.10:g.78184679C>T
  • NM_000199.3:c.1081G>A
  • NR_148201.2:n.995G>A
  • P51688:p.Val361Ile
Protein change:
V361I
Links:
UniProtKB: P51688#VAR_007415; dbSNP: rs9894254
NCBI 1000 Genomes Browser:
rs9894254
Molecular consequence:
  • NM_001352921.3:c.*168G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001352922.2:c.*131G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000199.5:c.1081G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148201.2:n.995G>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
SCV000695954Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Aug 22, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000801900Mayo Clinic Laboratories, Mayo Clinicno assertion criteria providedBenign
(Mar 16, 2017)
unknownclinical testing

SCV001797435Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695954.1

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

Description

Variant summary: The SGSH c.1081G>A (p.Val361Ile) variant causes a missense change involving a conserved nucleotide with 3/3 in silico tools (SNPs&GO and MutationTaster not captured here due to low reliability index and p-value, respectively) predict a benign outcome for this variant. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 6457/120406 (1/18, 258 homozygoes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic SGSH variant of 1/309 (0.0032275), suggesting this variant is likely a benign polymorphism. A reputable clinical laboratory cites the variant as "benign." Therefore, the variant of interest has been classified as Benign.

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801900.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001797435.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 24, 2021

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