NM_001352514.2(HLCS):c.2407C>T (p.Pro803Ser) AND Holocarboxylase synthetase deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 10, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001886030.6

Allele description [Variation Report for NM_001352514.2(HLCS):c.2407C>T (p.Pro803Ser)]

NM_001352514.2(HLCS):c.2407C>T (p.Pro803Ser)

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.2407C>T (p.Pro803Ser)

HGVS:

NC_000021.9:g.36756585G>A
NG_016193.2:g.238810C>T
NM_000411.8:c.1966C>T
NM_001242784.3:c.1966C>T
NM_001242785.2:c.1966C>T
NM_001352514.2:c.2407C>TMANE SELECT
NM_001352515.2:c.1966C>T
NM_001352516.2:c.1966C>T
NM_001352517.1:c.1966C>T
NM_001352518.2:c.1966C>T
NP_000402.3:p.Pro656Ser
NP_001229713.1:p.Pro656Ser
NP_001229714.1:p.Pro656Ser
NP_001339443.1:p.Pro803Ser
NP_001339444.1:p.Pro656Ser
NP_001339445.1:p.Pro656Ser
NP_001339446.1:p.Pro656Ser
NP_001339447.1:p.Pro656Ser
NC_000021.8:g.38128886G>A
NR_148020.2:n.2491C>T
NR_148021.1:n.2648C>T

Protein change:

P656S

Links:

dbSNP: rs538159086

NCBI 1000 Genomes Browser:

rs538159086

Molecular consequence:

NM_000411.8:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242784.3:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242785.2:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352514.2:c.2407C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352515.2:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352516.2:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352517.1:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352518.2:c.1966C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148020.2:n.2491C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.2648C>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
SCV002143528	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 10, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002815530	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 7, 2021)	unknown	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

SCV002143528

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 10, 2022)

germline

clinical testing

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

SCV002815530

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 7, 2021)

unknown

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
not provided	unknown	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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002143528.2

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 656 of the HLCS protein (p.Pro656Ser). This variant is present in population databases (rs538159086, gnomAD 0.09%). 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002815530.1

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

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

Last Updated: Sep 29, 2024

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