VCV002678212.3 - ClinVar

NM_000448.3(RAG1):c.2449del (p.Glu817fs)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Pathogenic/Likely pathogenic

2 out of 2 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_000448.3(RAG1):c.2449del (p.Glu817fs)

Variation ID: 2678212 Accession: VCV002678212.3

Type and length

Deletion, 1 bp

Location

Cytogenetic: 11p12 11: 36575750 (GRCh38) [ NCBI UCSC ] 11: 36597300 (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 30, 2023	Mar 4, 2025	Nov 30, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000448.3:c.2449del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000439.2:p.Glu817fs	frameshift
NM_001377277.1:c.2449del	NP_001364206.1:p.Glu817fs	frameshift
NM_001377278.1:c.2449del	NP_001364207.1:p.Glu817fs	frameshift
NM_001377279.1:c.2449del	NP_001364208.1:p.Glu817fs	frameshift
NM_001377280.1:c.2449del	NP_001364209.1:p.Glu817fs	frameshift
NC_000011.10:g.36575753del
NC_000011.9:g.36597303del
NG_007528.1:g.12741del
LRG_98:g.12741del
LRG_98t1:c.2449del	LRG_98p1:p.Glu817Lysfs

... more HGVS ... less HGVS

Protein change

E817fs

Other names

Canonical SPDI

NC_000011.10:36575749:GGGG:GGG

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

ClinGen: CA2613151028 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.
RAG1		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	898	928

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.
Combined immunodeficiency due to partial RAG1 deficiency	Likely pathogenic (1)	criteria provided, single submitter	Sep 9, 2022	RCV003472564.1
Combined immunodeficiency with skin granulomas Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	Pathogenic (1)	criteria provided, single submitter	Nov 30, 2023	RCV003779084.3

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.	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 (Sep 09, 2022) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Combined immunodeficiency due to partial RAG1 deficiency Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004200527.1 First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023
Pathogenic (Nov 30, 2023) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Combined immunodeficiency with skin granulomas Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004610119.2 First in ClinVar: Feb 28, 2024 Last updated: Mar 04, 2025	Publications: PubMed (1) PubMed: 33193364 Comment: This sequence change creates a premature translational stop signal (p.Glu817Lysfs28) in the RAG1 gene. While this is not anticipated to result in nonsense mediated decay, … (more) This sequence change creates a premature translational stop signal (p.Glu817Lysfs28) in the RAG1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 227 amino acid(s) of the RAG1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RAG1-related conditions. This variant disrupts a region of the RAG1 protein in which other variant(s) (p.His994Arg) have been determined to be pathogenic (PMID: 33193364; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change creates a premature translational stop signal (p.Glu817Lysfs*28) in the RAG1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 227 amino acid(s) of the RAG1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RAG1-related conditions. This variant disrupts a region of the RAG1 protein in which other variant(s) (p.His994Arg) have been determined to be pathogenic (PMID: 33193364; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

Title	Author	Journal	Year	Link
Vasculitis as a Major Morbidity Factor in Patients With Partial RAG Deficiency.	Geier CB	Frontiers in immunology	2020	PMID: 33193364

Text-mined citations for this variant ...

Record last updated Apr 08, 2025

ClinVar Genomic variation as it relates to human health

NM_000448.3(RAG1):c.2449del (p.Glu817fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...