NM_001352514.2(HLCS):c.1909C>T (p.Pro637Ser) AND Holocarboxylase synthetase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 22, 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:: RCV001883936.4

Allele description [Variation Report for NM_001352514.2(HLCS):c.1909C>T (p.Pro637Ser)]

NM_001352514.2(HLCS):c.1909C>T (p.Pro637Ser)

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.1909C>T (p.Pro637Ser)

HGVS:

NC_000021.9:g.36767269G>A
NG_016193.2:g.228126C>T
NM_000411.8:c.1468C>T
NM_001242784.3:c.1468C>T
NM_001242785.2:c.1468C>T
NM_001352514.2:c.1909C>TMANE SELECT
NM_001352515.2:c.1468C>T
NM_001352516.2:c.1468C>T
NM_001352517.1:c.1468C>T
NM_001352518.2:c.1468C>T
NP_000402.3:p.Pro490Ser
NP_001229713.1:p.Pro490Ser
NP_001229714.1:p.Pro490Ser
NP_001339443.1:p.Pro637Ser
NP_001339444.1:p.Pro490Ser
NP_001339445.1:p.Pro490Ser
NP_001339446.1:p.Pro490Ser
NP_001339447.1:p.Pro490Ser
NC_000021.8:g.38139570G>A
NR_148020.2:n.1768C>T
NR_148021.1:n.1925C>T

Protein change:

P490S

Links:

dbSNP: rs2145777265

NCBI 1000 Genomes Browser:

rs2145777265

Molecular consequence:

NM_000411.8:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242784.3:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242785.2:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352514.2:c.1909C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352515.2:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352516.2:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352517.1:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352518.2:c.1468C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148020.2:n.1768C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.1925C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002146911	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 22, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002146911

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 22, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002146911.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with HLCS-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HLCS protein function. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with serine at codon 490 of the HLCS protein (p.Pro490Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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