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NM_020661.4(AICDA):c.517T>G (p.Ser173Ala) AND Hyper-IgM syndrome type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 16, 2023
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:
RCV002770498.3

Allele description

NM_020661.4(AICDA):c.517T>G (p.Ser173Ala)

Gene:
AICDA:activation induced cytidine deaminase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.31
Genomic location:
Preferred name:
NM_020661.4(AICDA):c.517T>G (p.Ser173Ala)
HGVS:
  • NC_000012.12:g.8604833A>C
  • NG_011588.1:g.13014T>G
  • NM_001330343.2:c.487T>G
  • NM_020661.4:c.517T>GMANE SELECT
  • NP_001317272.1:p.Ser163Ala
  • NP_065712.1:p.Ser173Ala
  • NP_065712.1:p.Ser173Ala
  • LRG_17t1:c.517T>G
  • LRG_17:g.13014T>G
  • LRG_17p1:p.Ser173Ala
  • NC_000012.11:g.8757429A>C
  • NM_020661.2:c.517T>G
Protein change:
S163A
Molecular consequence:
  • NM_001330343.2:c.487T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020661.4:c.517T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hyper-IgM syndrome type 2
Synonyms:
Immunodeficiency with hyper IgM type 2; Hyper-IgM Immunodeficiency Syndrome, Type 2
Identifiers:
MONDO: MONDO:0011528; MedGen: C1720956; OMIM: 605258

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003021717Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 16, 2023) 		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 Invitae, SCV003021717.2

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

Description

An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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. ClinVar contains an entry for this variant (Variation ID: 1983875). This variant has not been reported in the literature in individuals affected with AICDA-related conditions. This variant is present in population databases (rs748806207, gnomAD 0.002%). This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 173 of the AICDA protein (p.Ser173Ala).

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

Last Updated: Jun 23, 2024