NM_005861.4(STUB1):c.535G>A (p.Glu179Lys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 3, 2024
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:
RCV003987995.1

Allele description [Variation Report for NM_005861.4(STUB1):c.535G>A (p.Glu179Lys)]

NM_005861.4(STUB1):c.535G>A (p.Glu179Lys)

Genes:
STUB1:STIP1 homology and U-box containing protein 1 [Gene - OMIM - HGNC]
JMJD8:jumonji domain containing 8 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_005861.4(STUB1):c.535G>A (p.Glu179Lys)
HGVS:
  • NC_000016.10:g.681803G>A
  • NG_034141.1:g.6693G>A
  • NG_132622.1:g.715G>A
  • NG_132622.2:g.735G>A
  • NG_132623.1:g.127G>A
  • NM_001005920.4:c.*991C>TMANE SELECT
  • NM_001293197.2:c.319G>A
  • NM_001323918.3:c.*1025C>T
  • NM_001323919.3:c.*991C>T
  • NM_001323920.3:c.*991C>T
  • NM_001323922.3:c.*1025C>T
  • NM_005861.4:c.535G>AMANE SELECT
  • NP_001280126.1:p.Glu107Lys
  • NP_005852.2:p.Glu179Lys
  • NC_000016.9:g.731803G>A
  • NM_005861.2:c.535G>A
  • NR_136650.3:n.1884C>T
  • NR_136651.3:n.1889C>T
  • NR_136652.3:n.1799C>T
Protein change:
E107K
Molecular consequence:
  • NM_001005920.4:c.*991C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001323918.3:c.*1025C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001323919.3:c.*991C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001323920.3:c.*991C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001323922.3:c.*1025C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001293197.2:c.319G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005861.4:c.535G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136650.3:n.1884C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136651.3:n.1889C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136652.3:n.1799C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004804014Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jan 3, 2024) 		germlineclinical testing

Citation Link

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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, SCV004804014.1

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

Description

Variant summary: STUB1 c.535G>A (p.Glu179Lys) results in a conservative amino acid change located in the CHIP, N-terminal tetratricopeptide repeat domain (IPR041312) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.1e-06 in 244806 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.535G>A in individuals affected with Autosomal Recessive Spinocerebellar Ataxia 16 and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 1, 2024