NM_000211.5(ITGB2):c.1537_1538del (p.Val513fs) AND Leukocyte adhesion deficiency 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 2, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001941551.5

Allele description [Variation Report for NM_000211.5(ITGB2):c.1537_1538del (p.Val513fs)]

NM_000211.5(ITGB2):c.1537_1538del (p.Val513fs)

Gene:

ITGB2:integrin subunit beta 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_000211.5(ITGB2):c.1537_1538del (p.Val513fs)

HGVS:

NC_000021.9:g.44890098CA[1]
NG_007270.2:g.43739GT[1]
NM_000211.5:c.1537_1538delMANE SELECT
NM_001127491.3:c.1537_1538del
NM_001303238.2:c.1330_1331del
NP_000202.3:p.Val513fs
NP_001120963.2:p.Val513fs
NP_001290167.1:p.Val444fs
LRG_76:g.43739GT[1]
NC_000021.8:g.46310012_46310013del
NC_000021.8:g.46310013CA[1]

Protein change:

V444fs

Links:

dbSNP: rs1230903176

NCBI 1000 Genomes Browser:

rs1230903176

Molecular consequence:

NM_000211.5:c.1537_1538del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127491.3:c.1537_1538del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001303238.2:c.1330_1331del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Leukocyte adhesion deficiency 1 (LAD1)
Synonyms:: LEUKOCYTE ADHESION DEFICIENCY, TYPE I; LAD 1; Lymphocyte function-associated antigen 1 immunodeficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007293; MedGen: C0398738; Orphanet: 2968; Orphanet: 99842; OMIM: 116920

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002236724	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 2, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 31374327, 22134107, 25703682, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002236724

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 2, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

A novel mutation of the ITGB2 gene in a Chinese Zhuang minority patient with leukocyte adhesion deficiency type 1 and glucose-6-phosphate dehydrogenase deficiency.

Zhang Y, Yang X, He X, Liu H, Guo P, Liu X, Xiao Y, Feng X, Wang Y, Li L.

Gene. 2019 Oct 5;715:144027. doi: 10.1016/j.gene.2019.144027. Epub 2019 Jul 30.

PubMed [citation]

PMID:: 31374327

Hematologically important mutations: leukocyte adhesion deficiency (first update).

van de Vijver E, Maddalena A, Sanal Ö, Holland SM, Uzel G, Madkaikar M, de Boer M, van Leeuwen K, Köker MY, Parvaneh N, Fischer A, Law SK, Klein N, Tezcan FI, Unal E, Patiroglu T, Belohradsky BH, Schwartz K, Somech R, Kuijpers TW, Roos D.

Blood Cells Mol Dis. 2012 Jan 15;48(1):53-61. doi: 10.1016/j.bcmd.2011.10.004. Epub 2011 Nov 30. Review.

PubMed [citation]

PMID:: 22134107
PMCID:: PMC4539347

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002236724.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with leukocyte adhesion deficiency type 1 (PMID: 31374327). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Val513Leufs*24) in the ITGB2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ITGB2 are known to be pathogenic (PMID: 22134107, 25703682).

#	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: Feb 20, 2024

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