VCV000895132.16 - ClinVar

NM_001352514.2(HLCS):c.574C>G (p.Pro192Ala)

Germline

Classification

criteria provided, conflicting classifications. Learn more about how ClinVar calculates review status.

Conflicting classifications of pathogenicity
Uncertain significance(3); Likely benign(1)

4 out of 4 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001352514.2(HLCS):c.574C>G (p.Pro192Ala)

Variation ID: 895132 Accession: VCV000895132.16

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 21q22.13 21: 36937312 (GRCh38) [ NCBI UCSC ] 21: 38309612 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	May 31, 2020	Jul 13, 2025	Mar 19, 2025

HGVS

Nucleotide	Protein	Molecular consequence
NM_001352514.2:c.574C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001339443.1:p.Pro192Ala	missense
NM_000411.8:c.133C>G	NP_000402.3:p.Pro45Ala	missense
NM_001242784.3:c.133C>G	NP_001229713.1:p.Pro45Ala	missense
NM_001242785.2:c.133C>G	NP_001229714.1:p.Pro45Ala	missense
NM_001352515.2:c.133C>G	NP_001339444.1:p.Pro45Ala	missense
NM_001352516.2:c.133C>G	NP_001339445.1:p.Pro45Ala	missense
NM_001352517.1:c.133C>G	NP_001339446.1:p.Pro45Ala	missense
NM_001352518.2:c.133C>G	NP_001339447.1:p.Pro45Ala	missense
NR_148020.2:n.433C>G		non-coding transcript variant
NR_148021.1:n.590C>G		non-coding transcript variant
NC_000021.9:g.36937312G>C
NC_000021.8:g.38309612G>C
NG_016193.2:g.58083C>G

... more HGVS ... less HGVS

Protein change

P192A, P45A

Other names

Canonical SPDI

NC_000021.9:36937311:G:C

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00004

Trans-Omics for Precision Medicine (TOPMed) 0.00006

The Genome Aggregation Database (gnomAD), exomes 0.00014

Exome Aggregation Consortium (ExAC) 0.00013

The Genome Aggregation Database (gnomAD) 0.00005

The Genome Aggregation Database (gnomAD), exomes 0.00012

Links

ClinGen: CA10020732 dbSNP: rs200950813 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
HLCS		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	1105	1205

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Holocarboxylase synthetase deficiency	Conflicting classifications of pathogenicity (2)	criteria provided, conflicting classifications	Oct 31, 2024	RCV001137044.15
not provided	Uncertain significance (1)	criteria provided, single submitter	Sep 26, 2024	RCV001732051.3
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Mar 19, 2025	RCV002556911.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Holocarboxylase synthetase deficiency	Illumina Laboratory Services, Illumina Accession: SCV001296935.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: show This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Sep 26, 2024) C Contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Not Provided	GeneDx Accession: SCV001982127.3 First in ClinVar: Oct 30, 2021 Last updated: Oct 08, 2024	Comment: show In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Likely benign (Oct 31, 2024) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Holocarboxylase synthetase deficiency	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001700956.5 First in ClinVar: Jun 08, 2021 Last updated: Feb 25, 2025	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Mar 19, 2025) C Contributing to aggregate classification	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Inborn genetic diseases	Ambry Genetics Accession: SCV003660360.3 First in ClinVar: Feb 07, 2023 Last updated: Jul 13, 2025	Comment: show The c.133C>G (p.P45A) alteration is located in exon 5 (coding exon 2) of the HLCS gene. This alteration results from a C to G substitution at nucleotide position 133, causing the proline (P) at amino acid position 45 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

Comment:

The c.133C>G (p.P45A) alteration is located in exon 5 (coding exon 2) of the HLCS gene. This alteration results from a C to G substitution at nucleotide position 133, causing the proline (P) at amino acid position 45 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs200950813 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 19, 2025