NM_001364905.1(LRBA):c.1923_1924+11del AND Common variable immunodeficiency 8, with autoimmunity

Clinical significance:Likely pathogenic (Last evaluated: Jun 25, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001244180.1

Allele description [Variation Report for NM_001364905.1(LRBA):c.1923_1924+11del]

NM_001364905.1(LRBA):c.1923_1924+11del

Gene:
LRBA:LPS responsive beige-like anchor protein [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4q31.3
Genomic location:
Preferred name:
NM_001364905.1(LRBA):c.1923_1924+11del
HGVS:
  • NC_000004.12:g.150900040_150900052del
  • NG_032855.1:g.120448_120460del
  • NM_001199282.2:c.1923_1924+11del
  • NM_001364905.1:c.1923_1924+11delMANE SELECT
  • NM_001367550.1:c.1923_1924+11del
  • NM_006726.4:c.1923_1924+11del
  • LRG_1324t1:c.1923_1924+11del
  • LRG_1324:g.120448_120460del
  • NC_000004.11:g.151821192_151821204del
  • NM_006726.4:c.1923_1924+11delAGGTATATAATTT
Molecular consequence:
  • NM_001199282.2:c.1923_1924+11del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001364905.1:c.1923_1924+11del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001367550.1:c.1923_1924+11del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_006726.4:c.1923_1924+11del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Common variable immunodeficiency 8, with autoimmunity (CVID8)
Identifiers:
MONDO: MONDO:0013863; MedGen: C3553512; Orphanet: 445018; OMIM: 614700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001417383Invitaecriteria provided, single submitter
Likely pathogenic
(Jun 25, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001417383.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant is a gross deletion of the genomic region encompassing part of exon 14 (c.1923_1924+11del) of the LRBA gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with LRBA-related disease. Loss-of-function variants in LRBA are known to be pathogenic (PMID: 26768763, 26206937, 25468195). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 19, 2020

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