U.S. flag

An official website of the United States government

NM_001099857.5(IKBKG):c.337G>A (p.Asp113Asn) AND Ectodermal dysplasia and immunodeficiency 1

Germline classification:
Likely benign (1 submission)
Last evaluated:
May 6, 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:
RCV002470750.9

Allele description [Variation Report for NM_001099857.5(IKBKG):c.337G>A (p.Asp113Asn)]

NM_001099857.5(IKBKG):c.337G>A (p.Asp113Asn)

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.337G>A (p.Asp113Asn)
HGVS:
  • NC_000023.11:g.154556314G>A
  • NG_009896.1:g.19071G>A
  • NM_001099856.6:c.541G>A
  • NM_001099857.5:c.337G>AMANE SELECT
  • NM_001145255.4:c.337G>A
  • NM_001321396.3:c.337G>A
  • NM_001321397.3:c.337G>A
  • NM_001377312.1:c.337G>A
  • NM_001377313.1:c.337G>A
  • NM_001377314.1:c.337G>A
  • NM_001377315.1:c.337G>A
  • NM_003639.4:c.337G>A
  • NP_001093326.2:p.Asp181Asn
  • NP_001093327.1:p.Asp113Asn
  • NP_001138727.1:p.Asp113Asn
  • NP_001308325.1:p.Asp113Asn
  • NP_001308326.1:p.Asp113Asn
  • NP_001364241.1:p.Asp113Asn
  • NP_001364242.1:p.Asp113Asn
  • NP_001364243.1:p.Asp113Asn
  • NP_001364244.1:p.Asp113Asn
  • NP_003630.1:p.Asp113Asn
  • LRG_70t1:c.337G>A
  • LRG_70:g.19071G>A
  • NC_000023.10:g.153784529G>A
  • NM_001099856.3:c.541G>A
  • NM_001099857.2:c.337G>A
  • NM_003639.3:c.337G>A
  • NR_165197.1:n.478G>A
  • Q9Y6K9:p.Asp113Asn
Protein change:
D113N; ASP113ASN
Links:
UniProtKB: Q9Y6K9#VAR_026493; UniProtKB/Swiss-Prot: VAR_026493; OMIM: 300248.0032; dbSNP: rs179363896
NCBI 1000 Genomes Browser:
rs179363896
Molecular consequence:
  • NM_001099856.6:c.541G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099857.5:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145255.4:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321396.3:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321397.3:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377312.1:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377313.1:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377314.1:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377315.1:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003639.4:c.337G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_165197.1:n.478G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002769322Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(May 6, 2021)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Functional Evaluation of an IKBKG Variant Suspected to Cause Immunodeficiency Without Ectodermal Dysplasia.

Frans G, van der Werff Ten Bosch J, Moens L, Gijsbers R, Changi-Ashtiani M, Rokni-Zadeh H, Shahrooei M, Wuyts G, Meyts I, Bossuyt X.

J Clin Immunol. 2017 Nov;37(8):801-810. doi: 10.1007/s10875-017-0448-9. Epub 2017 Oct 10.

PubMed [citation]
PMID:
28993958

Rescue of recurrent deep intronic mutation underlying cell type-dependent quantitative NEMO deficiency.

Boisson B, Honda Y, Ajiro M, Bustamante J, Bendavid M, Gennery AR, Kawasaki Y, Ichishima J, Osawa M, Nihira H, Shiba T, Tanaka T, Chrabieh M, Bigio B, Hur H, Itan Y, Liang Y, Okada S, Izawa K, Nishikomori R, Ohara O, Heike T, et al.

J Clin Invest. 2019 Feb 1;129(2):583-597. doi: 10.1172/JCI124011. Epub 2018 Dec 18.

PubMed [citation]
PMID:
30422821
PMCID:
PMC6355244
See all PubMed Citations (5)

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769322.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely benign. Following criteria are met: 0109 - This gene is associated with X-linked recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to asparagine. (I) 0308 - Population frequency for this variant is out of keeping with known incidence of Immunodeficiency 3 (MIM#3300636) and ectodermal dysplasia and immunodeficiency 1 (MIM#300291). (SB) 0504 - Same amino acid change has been observed in placental mammals. (SB) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has previously been reported as likely benign and as a variant of uncertain significance (ClinVar). However, it has more recently been suggested to be non disease-causing due to population frequency (PMID: 33224153; 30422821). In addition, this variant was identified in a patient with recurrent bacterial and viral infections since his third month of life but the variant was also identified is the proband's 40 year old healthy cousin (PMID: 31965418) (I) 1004 - This variant has moderate functional evidence supporting normal protein function (PMID: 28993958). (SB) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Nov 24, 2024