NM_001352514.2(HLCS):c.1223del (p.Gly408fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 21, 2016)

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_001352514.2(HLCS):c.1223del (p.Gly408fs)]

NM_001352514.2(HLCS):c.1223del (p.Gly408fs)

HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_001352514.2(HLCS):c.1223del (p.Gly408fs)
  • NC_000021.9:g.36936665del
  • NG_016193.2:g.58732del
  • NM_000411.8:c.782del
  • NM_001242784.3:c.782del
  • NM_001242785.2:c.782del
  • NM_001352514.2:c.1223delMANE SELECT
  • NM_001352515.2:c.782del
  • NM_001352516.2:c.782del
  • NM_001352517.1:c.782del
  • NM_001352518.1:c.782del
  • NP_000402.3:p.Gly261fs
  • NP_001229713.1:p.Gly261fs
  • NP_001229714.1:p.Gly261fs
  • NP_001339443.1:p.Gly408fs
  • NP_001339444.1:p.Gly261fs
  • NP_001339445.1:p.Gly261fs
  • NP_001339446.1:p.Gly261fs
  • NP_001339447.1:p.Gly261fs
  • NC_000021.8:g.38308963del
  • NC_000021.8:g.38308965del
  • NM_000411.6:c.782del
  • NM_000411.6:c.782delG
  • NM_000411.8:c.782delG
  • NR_148020.2:n.1082del
  • NR_148021.1:n.1239del
  • p.G261VfsX20
Protein change:
dbSNP: rs771944310
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000411.8:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001242784.3:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001242785.2:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352514.2:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352515.2:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352516.2:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352517.1:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001352518.1:c.782del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148020.2:n.1082del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148021.1:n.1239del - non-coding transcript variant - [Sequence Ontology: SO:0001619]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000238927GeneDxcriteria provided, single submitter
(Sep 21, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000238927.8

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


The c.782delG deletion pathogenic variant in the HLCS gene have been reported previously in association with holocarboxylase synthetase (HLCS) deficiency (Suzuki et al., 2005). The c.782delG deletion causes a frameshift starting with codon Glycine 261, changes this amino acid to a Valine residue and creates a premature Stop codon at position 20 of the new reading frame, denoted p.Gly261ValfsX20. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.

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

Last Updated: Aug 27, 2021

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