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NM_001352514.2(HLCS):c.2036C>A (p.Ser679Tyr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 22, 2018
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:
RCV000489053.2

Allele description [Variation Report for NM_001352514.2(HLCS):c.2036C>A (p.Ser679Tyr)]

NM_001352514.2(HLCS):c.2036C>A (p.Ser679Tyr)

Gene:
HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.13
Genomic location:
Preferred name:
NM_001352514.2(HLCS):c.2036C>A (p.Ser679Tyr)
HGVS:
  • NC_000021.9:g.36765097G>T
  • NG_016193.2:g.230298C>A
  • NM_000411.8:c.1595C>A
  • NM_001242784.3:c.1595C>A
  • NM_001242785.2:c.1595C>A
  • NM_001352514.2:c.2036C>AMANE SELECT
  • NM_001352515.2:c.1595C>A
  • NM_001352516.2:c.1595C>A
  • NM_001352517.1:c.1595C>A
  • NM_001352518.2:c.1595C>A
  • NP_000402.3:p.Ser532Tyr
  • NP_001229713.1:p.Ser532Tyr
  • NP_001229714.1:p.Ser532Tyr
  • NP_001339443.1:p.Ser679Tyr
  • NP_001339444.1:p.Ser532Tyr
  • NP_001339445.1:p.Ser532Tyr
  • NP_001339446.1:p.Ser532Tyr
  • NP_001339447.1:p.Ser532Tyr
  • NC_000021.8:g.38137398G>T
  • NM_000411.6:c.1595C>A
  • NR_148020.2:n.1895C>A
  • NR_148021.1:n.2052C>A
Protein change:
S532Y
Links:
dbSNP: rs777373322
NCBI 1000 Genomes Browser:
rs777373322
Molecular consequence:
  • NM_000411.8:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001242784.3:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001242785.2:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352514.2:c.2036C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352515.2:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352516.2:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352517.1:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352518.2:c.1595C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148020.2:n.1895C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148021.1:n.2052C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000577091GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 22, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000577091.4

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

Description

The S532Y variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S532Y variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S532Y variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Sep 29, 2024