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NC_000022.10:g.(?_23915453)_(24237293_?)del AND Agammaglobulinemia 2, autosomal recessive

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 20, 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:
RCV001941512.4

Allele description [Variation Report for NC_000022.10:g.(?_23915453)_(24237293_?)del]

NC_000022.10:g.(?_23915453)_(24237293_?)del

Genes:
  • SMARCB1:SWI/SNF related BAF chromatin remodeling complex subunit B1 [Gene - OMIM - HGNC]
  • VPREB3:V-set pre-B cell surrogate light chain 3 [Gene - OMIM - HGNC]
  • DRICH1:aspartate rich 1 [Gene - HGNC]
  • C22orf15:chromosome 22 open reading frame 15 [Gene - HGNC]
  • CHCHD10:coiled-coil-helix-coiled-coil-helix domain containing 10 [Gene - OMIM - HGNC]
  • DERL3:derlin 3 [Gene - OMIM - HGNC]
  • IGLL1:immunoglobulin lambda like polypeptide 1 [Gene - OMIM - HGNC]
  • MIF:macrophage migration inhibitory factor [Gene - OMIM - HGNC]
  • MMP11:matrix metallopeptidase 11 [Gene - OMIM - HGNC]
  • RGL4:ral guanine nucleotide dissociation stimulator like 4 [Gene - OMIM - HGNC]
  • SLC2A11:solute carrier family 2 member 11 [Gene - OMIM - HGNC]
  • ZNF70:zinc finger protein 70 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q11.23
Genomic location:
Chr22: 23915453 - 24237293 (on Assembly GRCh37)
Preferred name:
NC_000022.10:g.(?_23915453)_(24237293_?)del
HGVS:
NC_000022.10:g.(?_23915453)_(24237293_?)del

Condition(s)

Name:
Agammaglobulinemia 2, autosomal recessive (AGM2)
Synonyms:
AGAMMAGLOBULINEMIA, AUTOSOMAL RECESSIVE, DUE TO IGLL1 DEFECT
Identifiers:
MONDO: MONDO:0013287; MedGen: C3150750; OMIM: 613500

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002223760Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 20, 2021) 		germlineclinical testing

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

Help

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002223760.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the IGLL1 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in IGLL1 cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with IGLL1-related conditions. 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.

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

Last Updated: Sep 29, 2024