VCV001741699.4 - ClinVar

NM_001123385.2(BCOR):c.458C>T (p.Pro153Leu)

Germline

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.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001123385.2(BCOR):c.458C>T (p.Pro153Leu)

Variation ID: 1741699 Accession: VCV001741699.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp11.4 X: 40074888 (GRCh38) [ NCBI UCSC ] X: 39934141 (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	Nov 29, 2022	May 1, 2024	Jan 24, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001123385.2:c.458C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001116857.1:p.Pro153Leu	missense
NM_001123383.1:c.458C>T	NP_001116855.1:p.Pro153Leu	missense
NM_001123384.2:c.458C>T	NP_001116856.1:p.Pro153Leu	missense
NM_017745.5:c.458C>T
NM_017745.6:c.458C>T	NP_060215.4:p.Pro153Leu	missense
NC_000023.11:g.40074888G>A
NC_000023.10:g.39934141G>A
NG_008880.1:g.107442C>T
NG_087735.1:g.1248G>A
LRG_627:g.107442C>T
LRG_627t1:c.458C>T	LRG_627p1:p.Pro153Leu
LRG_627t2:c.458C>T	LRG_627p2:p.Pro153Leu

... more HGVS ... less HGVS

Protein change

P153L

Other names

Canonical SPDI

NC_000023.11:40074887:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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.

Links

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.
BCOR		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	502	800
LOC126863239	-	-	-	GRCh38	-	221

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.
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Sep 22, 2016	RCV002342266.2
not provided	Uncertain significance (1)	criteria provided, single submitter	Aug 23, 2022	RCV003128953.1
BCOR-related disorder	Uncertain significance (1)	criteria provided, single submitter	Jan 24, 2023	RCV004548277.1

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.	More information 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 (Aug 23, 2022)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003806139.1 First in ClinVar: Mar 04, 2023 Last updated: Mar 04, 2023	Comment: Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; … (more) Not observed at significant frequency in large population cohorts (gnomAD); 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)
Uncertain significance (Jan 24, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	BCOR-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004117449.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The BCOR c.458C>T variant is predicted to result in the amino acid substitution p.Pro153Leu. To our knowledge, this variant has not been reported in the … (more) The BCOR c.458C>T variant is predicted to result in the amino acid substitution p.Pro153Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0036% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-39934141-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)
Uncertain significance (Sep 22, 2016)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002636317.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: The p.P153L variant (also known as c.458C>T), located in coding exon 3 of the BCOR gene, results from a C to T substitution at nucleotide … (more) The p.P153L variant (also known as c.458C>T), located in coding exon 3 of the BCOR gene, results from a C to T substitution at nucleotide position 458. The proline at codon 153 is replaced by leucine, an amino acid with some similar properties. This variant did not co-segregate with disease in one family tested in our laboratory. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6502 samples with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear. (less)

Comment:

Not observed at significant frequency in large population cohorts (gnomAD); 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

Comment:

The BCOR c.458C>T variant is predicted to result in the amino acid substitution p.Pro153Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0036% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-39934141-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Comment:

The p.P153L variant (also known as c.458C>T), located in coding exon 3 of the BCOR gene, results from a C to T substitution at nucleotide position 458. The proline at codon 153 is replaced by leucine, an amino acid with some similar properties. This variant did not co-segregate with disease in one family tested in our laboratory. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6502 samples with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

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 this variant ...

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001123385.2(BCOR):c.458C>T (p.Pro153Leu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...