NM_000520.6(HEXA):c.103C>T (p.Gln35Ter) AND Tay-Sachs disease

Clinical significance:Likely pathogenic (Last evaluated: Nov 4, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000520.6(HEXA):c.103C>T (p.Gln35Ter)]

NM_000520.6(HEXA):c.103C>T (p.Gln35Ter)

HEXA:hexosaminidase subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000520.6(HEXA):c.103C>T (p.Gln35Ter)
  • NC_000015.10:g.72375870G>A
  • NG_009017.1:g.5310C>T
  • NG_009017.2:g.5310C>T
  • NM_000520.6:c.103C>TMANE SELECT
  • NM_001318825.2:c.103C>T
  • NP_000511.2:p.Gln35Ter
  • NP_001305754.1:p.Gln35Ter
  • NC_000015.9:g.72668211G>A
  • NM_000520.5:c.103C>T
  • NR_134869.3:n.145C>T
Protein change:
Molecular consequence:
  • NR_134869.3:n.145C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000520.6:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001318825.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]


Tay-Sachs disease (TSD)
GM2 gangliosidosis, type 1; HexA deficiency; Hexosaminidase alpha-subunit deficiency (variant B); See all synonyms [MedGen]
MONDO: MONDO:0010100; MedGen: C0039373; Orphanet: 845; OMIM: 272800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001448578Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Nov 4, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001448578.1

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


Variant summary: HEXA c.103C>T (p.Gln35X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations upstream and downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251410 control chromosomes (gnomAD). To our knowledge, no occurrence of c.103C>T in individuals affected with Tay-Sachs Disease and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Jun 14, 2021

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