VCV002672188.2 - ClinVar

NM_003120.3(SPI1):c.689G>C (p.Arg230Pro)

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.

(2)

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.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_003120.3(SPI1):c.689G>C (p.Arg230Pro)

Variation ID: 2672188 Accession: VCV002672188.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11p11.2 11: 47355351 (GRCh38) [ NCBI UCSC ] 11: 47376902 (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	Dec 25, 2023	Nov 10, 2024	Mar 6, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_003120.3:c.689G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_003111.2:p.Arg230Pro	missense
NM_001080547.1:c.692G>C
NM_001080547.2:c.692G>C	NP_001074016.1:p.Arg231Pro	missense
NC_000011.10:g.47355351C>G
NC_000011.9:g.47376902C>G
NG_007667.1:g.2352G>C
LRG_386:g.2352G>C

... more HGVS ... less HGVS

Protein change

R230P, R231P

Other names

Canonical SPDI

NC_000011.10:47355350:C:G

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.
SPI1		-	-	GRCh38 GRCh37	27	43

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.
Agammaglobulinemia 10, autosomal dominant	Likely pathogenic (1)	criteria provided, single submitter	Jul 26, 2023	RCV003459002.1
not provided	Uncertain significance (1)	criteria provided, single submitter	Mar 6, 2024	RCV004780556.1

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.
Likely pathogenic (Jul 26, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Agammaglobulinemia 10, autosomal dominant Affected status: yes Allele origin: germline	Clinical Genomics Laboratory, Washington University in St. Louis Accession: SCV004177140.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023	Comment: The SPI1 c.689G>C (p.Arg230Pro) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), … (more) The SPI1 c.689G>C (p.Arg230Pro) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. The arginine at this codon occurs in the ETS domain, responsible for DNA binding, and computational predictors indicate that the variant is damaging, evidence that correlates with impact to SPI1 function. In support of this prediction, functional studies show substitution of this arginine results in decreased immune system activation, indicating that this variant impacts protein function (Ha SD et al., PMID: 31586032). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic. (less)
Uncertain significance (Mar 06, 2024)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV005389212.1 First in ClinVar: Nov 10, 2024 Last updated: Nov 10, 2024	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)

Comment:

The SPI1 c.689G>C (p.Arg230Pro) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. The arginine at this codon occurs in the ETS domain, responsible for DNA binding, and computational predictors indicate that the variant is damaging, evidence that correlates with impact to SPI1 function. In support of this prediction, functional studies show substitution of this arginine results in decreased immune system activation, indicating that this variant impacts protein function (Ha SD et al., PMID: 31586032). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic.

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

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 10, 2024

ClinVar Genomic variation as it relates to human health

NM_003120.3(SPI1):c.689G>C (p.Arg230Pro)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...