NM_001364905.1(LRBA):c.1879G>A (p.Ala627Thr) AND Combined immunodeficiency due to LRBA deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 25, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001217425.11

Allele description [Variation Report for NM_001364905.1(LRBA):c.1879G>A (p.Ala627Thr)]

NM_001364905.1(LRBA):c.1879G>A (p.Ala627Thr)

Gene:

LRBA:LPS responsive beige-like anchor protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q31.3

Genomic location:

Preferred name:

NM_001364905.1(LRBA):c.1879G>A (p.Ala627Thr)

HGVS:

NC_000004.12:g.150900094C>T
NG_032855.1:g.120404G>A
NM_001199282.2:c.1879G>A
NM_001364905.1:c.1879G>AMANE SELECT
NM_001367550.1:c.1879G>A
NM_006726.4:c.1879G>A
NP_001186211.2:p.Ala627Thr
NP_001351834.1:p.Ala627Thr
NP_001354479.1:p.Ala627Thr
NP_006717.2:p.Ala627Thr
LRG_1324t1:c.1879G>A
LRG_1324:g.120404G>A
LRG_1324p1:p.Ala627Thr
NC_000004.11:g.151821246C>T

Protein change:

A627T

Links:

dbSNP: rs550423754

NCBI 1000 Genomes Browser:

rs550423754

Molecular consequence:

NM_001199282.2:c.1879G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364905.1:c.1879G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001367550.1:c.1879G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006726.4:c.1879G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Combined immunodeficiency due to LRBA deficiency
Synonyms:: Common variable immunodeficiency 8, with autoimmunity
Identifiers:: MONDO: MONDO:0013863; MedGen: C3553512; Orphanet: 445018; OMIM: 614700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001389263	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 9, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003817065	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 25, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001389263

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 9, 2020)

germline

clinical testing

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

SCV003817065

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 25, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001389263.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces alanine with threonine at codon 627 of the LRBA protein (p.Ala627Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with LRBA-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003817065.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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