RGD:8563512 Rat Genome Database

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Variant: RGD:8563512 - Homo sapiens

RGD ID:

8563512

RS ID:

rs121918575

ClinVar ID:

CV28177

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

RAG2

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	11	36,614,367
GRCh38	11	36,592,817

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

ClinVar Data

HGVS Name(s)	Last Evaluated	Molecular Consequence	Clinical Significance	Trait Synonyms
LRG_99:g.10420G>C NG_007573.1:g.10420G>C NC_000011.10:g.36592817C>G NC_000011.9:g.36614367C>G More...	11/14/2023	2kb upstream variant\|missense\|missense variant	pathogenic\|likely pathogenic\|uncertain significance	Bubble boy disease; Combined cellular and humoral immune defects with granulomas; Common variable agammaglobulinemia; Common variable hypogamma-globulinemia; Inborn error of immunity; Inborn errors of immunity; none provided; Primary immunodeficiency; RAG2 deficiency; Recombinase activating gene 2 deficiency; SCID, AR, T-cell negative, B-cell negative, NK cell-positive; SCID, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-POSITIVE; Severe Combined Immune Deficiency; Severe combined immunodeficiency; Severe combined immunodeficiency due to complete RAG1/2 deficiency; SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-POSITIVE; Severe immunodeficiency, autosomal recessive, T-cell negative, B-cell negative, NK cell-positive

Disease Annotations Click to see Annotation Detail View

combined cellular and humoral immune defects with granulomas (IAGP)

common variable immunodeficiency (IAGP)

recombinase activating gene 2 deficiency (IAGP)

severe combined immunodeficiency (IAGP)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Severe combined immunodeficiency (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	RAG2
Accession:	XM_047427385
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	451

Amino Acid Sequence (Calculated using NCBI transcript definition)
MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPTIFSKDSCYLPPLRYPATCTF KGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKVTFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRS YMPSTHRTTEKWNSVADCLPCVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIREMETPDWTPDIKHSKIWFGS NMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQTTFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFD TYNEDDEEDESETGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDAHWVHAQCMDLAERTLIHLSAGSNKYYCNE HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD*

Gene Symbol:	RAG2
Accession:	NM_001243786
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	451

Amino Acid Sequence (Calculated using NCBI transcript definition)
MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPTIFSKDSCYLPPLRYPATCTF KGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKVTFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRS YMPSTHRTTEKWNSVADCLPCVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIREMETPDWTPDIKHSKIWFGS NMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQTTFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFD TYNEDDEEDESETGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDAHWVHAQCMDLAERTLIHLSAGSNKYYCNE HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD*

Gene Symbol:	RAG2
Accession:	XM_047427386
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	451

Amino Acid Sequence (Calculated using NCBI transcript definition)
MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPTIFSKDSCYLPPLRYPATCTF KGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKVTFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRS YMPSTHRTTEKWNSVADCLPCVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIREMETPDWTPDIKHSKIWFGS NMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQTTFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFD TYNEDDEEDESETGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDAHWVHAQCMDLAERTLIHLSAGSNKYYCNE HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD*

Gene Symbol:	RAG2
Accession:	NM_000536
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	451

Amino Acid Sequence (Calculated using NCBI transcript definition)
MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPTIFSKDSCYLPPLRYPATCTF KGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKVTFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRS YMPSTHRTTEKWNSVADCLPCVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIREMETPDWTPDIKHSKIWFGS NMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQTTFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFD TYNEDDEEDESETGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDAHWVHAQCMDLAERTLIHLSAGSNKYYCNE HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD*

Gene Symbol:	RAG2
Accession:	NM_001243785
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	451

Amino Acid Sequence (Calculated using NCBI transcript definition)
MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPTIFSKDSCYLPPLRYPATCTF KGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKVTFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRS YMPSTHRTTEKWNSVADCLPCVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIREMETPDWTPDIKHSKIWFGS NMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQTTFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFD TYNEDDEEDESETGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDAHWVHAQCMDLAERTLIHLSAGSNKYYCNE HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD*

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional References at PubMed

PMID:18463379	PMID:21664875	PMID:24331380	PMID:24996264	PMID:25741868	PMID:26457731	PMID:26996199	PMID:28492532	PMID:29772310	PMID:31334206	PMID:31388879	PMID:32581362
PMID:32655540

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000014020	CLINVAR
	RCV000521152	CLINVAR
	RCV000681597	CLINVAR
	RCV000821298	CLINVAR
	RCV001027616	CLINVAR
	RCV001731284	CLINVAR
	RCV003398501	CLINVAR
dbSNP (RS)	rs121918575	CLINVAR
MedGen	C0009447	CLINVAR
	C0085110	CLINVAR
	C2673536	CLINVAR
	C3661900	CLINVAR
	CN257931	CLINVAR
NCBI Gene	RAG2	CLINVAR
OMIM	179616	CLINVAR
	233650	CLINVAR
	601457	CLINVAR
OMIM Allele	179616.0010	CLINVAR
SNOMED CT	191010004	CLINVAR
	31323000	CLINVAR

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

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MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Variant: RGD:8563512 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar

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Variant: RGD:8563512 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar