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NM_001099857.5(IKBKG):c.399+6C>T AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 16, 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:
RCV001839197.2

Allele description [Variation Report for NM_001099857.5(IKBKG):c.399+6C>T]

NM_001099857.5(IKBKG):c.399+6C>T

Gene:
IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001099857.5(IKBKG):c.399+6C>T
HGVS:
  • NC_000023.11:g.154556382C>T
  • NG_009896.1:g.19139C>T
  • NM_001099856.6:c.603+6C>T
  • NM_001099857.5:c.399+6C>TMANE SELECT
  • NM_001145255.4:c.399+6C>T
  • NM_001321396.3:c.399+6C>T
  • NM_001321397.3:c.399+6C>T
  • NM_001377312.1:c.399+6C>T
  • NM_001377313.1:c.399+6C>T
  • NM_001377314.1:c.399+6C>T
  • NM_001377315.1:c.399+6C>T
  • NM_003639.4:c.399+6C>T
  • LRG_70:g.19139C>T
  • NC_000023.10:g.153784597C>T
Links:
dbSNP: rs1557236080
NCBI 1000 Genomes Browser:
rs1557236080
Molecular consequence:
  • NM_001099856.6:c.603+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001099857.5:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145255.4:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001321396.3:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001321397.3:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377312.1:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377313.1:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377314.1:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377315.1:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003639.4:c.399+6C>T - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Immunodeficiency 33 (IMD33)
Synonyms:
Immunodeficiency without anhidrotic ectodermal dysplasia; X-linked mendelian susceptibility to mycobacterial diseases due to IKBKG deficiency
Identifiers:
MONDO: MONDO:0010386; MedGen: C1970879; Orphanet: 319605; Orphanet: 319612; OMIM: 300636
Name:
Ectodermal dysplasia and immunodeficiency 1 (EDAID1)
Synonyms:
Ectodermal dysplasia, anhidrotic, with immunodeficiency, osteopetrosis, and lymphedema; ECTODERMAL DYSPLASIA AND IMMUNE DEFICIENCY 1; Hyper-IgM immunodeficiency, X-linked, with hypohidrotic ectodermal dysplasia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020740; MedGen: C1846008; Orphanet: 238468; Orphanet: 98813; OMIM: 300291

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002099141New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Apr 16, 2021) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002099141.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited hemizygous c.399+6C>T splice-region variant identified in intron 3 (of 9) the IKBKG gene has not been reported in affected individuals in the literature. The variant is absent from the gnomAD(v3) database suggesting it is not a common benign variant in populations represented inthat database. In silico tools provide conflicting predictions about potential effect(s) of this variant on normal mRNA splicing. Based on the available evidence, the inherited hemizygous c.399+6C>T splice-region variant identified in the IKBKG gene is reported as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 22, 2024