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NM_001364905.1(LRBA):c.2166-1G>C

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
May 21, 2020
Accession:
VCV001066609.1
Variation ID:
1066609
Description:
single nucleotide variant
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NM_001364905.1(LRBA):c.2166-1G>C

Allele ID
1055406
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4q31.3
Genomic location
4: 150872756 (GRCh38) GRCh38 UCSC
4: 151793908 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.151793908C>G
NC_000004.12:g.150872756C>G
NM_001364905.1:c.2166-1G>C MANE Select splice acceptor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000004.12:150872755:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter May 21, 2020 RCV001377647.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LRBA - - GRCh38
GRCh37
910 974

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 21, 2020)
criteria provided, single submitter
Method: clinical testing
Common variable immunodeficiency 8, with autoimmunity
Allele origin: germline
Invitae
Accession: SCV001575030.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects an acceptor splice site in intron 17 of the LRBA gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
The extended phenotype of LPS-responsive beige-like anchor protein (LRBA) deficiency. Gámez-Díaz L The Journal of allergy and clinical immunology 2016 PMID: 26768763
AUTOIMMUNE DISEASE. Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive to abatacept therapy. Lo B Science (New York, N.Y.) 2015 PMID: 26206937
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Record last updated May 13, 2021