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NM_001352514.2(HLCS):c.1233C>A (p.His411Gln) AND Holocarboxylase synthetase deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 26, 2021
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:
RCV001343560.6

Allele description [Variation Report for NM_001352514.2(HLCS):c.1233C>A (p.His411Gln)]

NM_001352514.2(HLCS):c.1233C>A (p.His411Gln)

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.1233C>A (p.His411Gln)
HGVS:
  • NC_000021.9:g.36936653G>T
  • NG_016193.2:g.58742C>A
  • NM_000411.8:c.792C>A
  • NM_001242784.3:c.792C>A
  • NM_001242785.2:c.792C>A
  • NM_001352514.2:c.1233C>AMANE SELECT
  • NM_001352515.2:c.792C>A
  • NM_001352516.2:c.792C>A
  • NM_001352517.1:c.792C>A
  • NM_001352518.2:c.792C>A
  • NP_000402.3:p.His264Gln
  • NP_001229713.1:p.His264Gln
  • NP_001229714.1:p.His264Gln
  • NP_001339443.1:p.His411Gln
  • NP_001339444.1:p.His264Gln
  • NP_001339445.1:p.His264Gln
  • NP_001339446.1:p.His264Gln
  • NP_001339447.1:p.His264Gln
  • NC_000021.8:g.38308953G>T
  • NR_148020.2:n.1092C>A
  • NR_148021.1:n.1249C>A
Protein change:
H264Q
Links:
dbSNP: rs1601802008
NCBI 1000 Genomes Browser:
rs1601802008
Molecular consequence:
  • NM_000411.8:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001242784.3:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001242785.2:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352514.2:c.1233C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352515.2:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352516.2:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352517.1:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352518.2:c.792C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148020.2:n.1092C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148021.1:n.1249C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Holocarboxylase synthetase deficiency
Synonyms:
MULTIPLE CARBOXYLASE DEFICIENCY, EARLY ONSET
Identifiers:
MONDO: MONDO:0009666; MedGen: C0268581; Orphanet: 79242; OMIM: 253270

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001537548Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Aug 26, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001537548.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces histidine with glutamine at codon 264 of the HLCS protein (p.His264Gln). The histidine residue is weakly conserved and there is a small physicochemical difference between histidine and glutamine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with HLCS-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024