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NM_001282225.2(ADA2):c.506G>A (p.Arg169Gln) AND Vasculitis due to ADA2 deficiency

Germline classification:
Pathogenic (9 submissions)
Last evaluated:
Sep 24, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000106384.25

Allele description [Variation Report for NM_001282225.2(ADA2):c.506G>A (p.Arg169Gln)]

NM_001282225.2(ADA2):c.506G>A (p.Arg169Gln)

Gene:
ADA2:adenosine deaminase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q11.1
Genomic location:
Preferred name:
NM_001282225.2(ADA2):c.506G>A (p.Arg169Gln)
Other names:
ADA2, ARG169GLN (rs77563738)
HGVS:
  • NC_000022.11:g.17207107C>T
  • NG_033943.1:g.19748G>A
  • NM_001282225.2:c.506G>AMANE SELECT
  • NM_001282226.2:c.506G>A
  • NM_001282227.2:c.380G>A
  • NM_001282228.2:c.380G>A
  • NM_001282229.2:c.146G>A
  • NP_001269154.1:p.Arg169Gln
  • NP_001269155.1:p.Arg169Gln
  • NP_001269156.1:p.Arg127Gln
  • NP_001269157.1:p.Arg127Gln
  • NP_001269158.1:p.Arg49Gln
  • LRG_1217t1:c.506G>A
  • LRG_1217:g.19748G>A
  • LRG_1217p1:p.Arg169Gln
  • NC_000022.10:g.17687997C>T
  • NM_001282225.1:c.506G>A
  • p.Arg169Gln
Protein change:
R127Q; ARG169GLN
Links:
OMIM: 607575.0005; dbSNP: rs77563738
NCBI 1000 Genomes Browser:
rs77563738
Molecular consequence:
  • NM_001282225.2:c.506G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282226.2:c.506G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282227.2:c.380G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282228.2:c.380G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282229.2:c.146G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Vasculitis due to ADA2 deficiency (VAIHS)
Synonyms:
Polyarteritis nodosa, childhoood-onset; VASCULITIS, AUTOINFLAMMATION, IMMUNODEFICIENCY, AND HEMATOLOGIC DEFECTS SYNDROME
Identifiers:
MONDO: MONDO:0014306; MedGen: C3887654; Orphanet: 404553; OMIM: 615688

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000143888OMIM
no assertion criteria provided
Pathogenic
(Mar 6, 2014)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000773923Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 29, 2024)
germlineclinical testing

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

SCV000994598GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV001448498Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Nov 24, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001469045Johns Hopkins Genomics, Johns Hopkins University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 2, 2020)
germlineclinical testing

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

SCV001760481Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Likely pathogenicgermlineclinical testing

Citation Link,

SCV002059413Centogene AG - the Rare Disease Company
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 6, 2017)
germlineclinical testing

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

SCV003836134Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 8, 2022)
unknownclinical testing

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

SCV005326547Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 24, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedunknownunknownnot 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

Adenosine Deaminase 2 Deficiency.

Aksentijevich I, Sampaio Moura N, Barron K.

2019 Aug 8. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]
PMID:
31393689
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000143888.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a patient with vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome (VAIHS; 615688), Zhou et al. (2014) identified compound heterozygous mutations in the CECR1 gene: a c.506G-A transition in exon 3, resulting in an arg169-to-gln (R169Q) substitution in the PRB domain, and Y453C (607575.0001). Another patient with the disorder was compound heterozygous for R169Q and an intragenic 28-kb deletion. Both mutations occurred at highly conserved residues. Haplotype analysis indicated a founder effect for the R169Q mutation. The R169Q mutation was present in less than 1% of alleles in the 1000 Genomes Project and Exome Variant Server databases; it was not present in the ClinSeq 801 database.

In 4 German sibs with polyarteritis nodosa, Navon Elkan et al. (2014) identified compound heterozygous mutations in the CECR1 gene: R169Q and a c.752C-T transition, resulting in a pro251-to-leu (P251L; 607575.0007) substitution at a highly conserved residue. Each unaffected parent was heterozygous for 1 of the mutations. Among 4,300 European controls, the R169Q variant was found in 7 (0.0008) and the P251L variant was found in 1 (0.0001). Serum ADA2 activity in patients was severely reduced compared to controls. The R169Q protein was barely detectable in transfected cells.

Van Montfrans et al. (2016) identified a homozygous R169Q mutation in the ADA2 gene in 9 patients from 6 unrelated families from the Netherlands with highly variable presentations and manifestations. ADA2 enzyme activity in patients was significantly decreased compared with healthy controls. ADA2 activity levels tended to be lower in patients with stroke compared with patients without stroke.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000773923.7

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 169 of the ADA2 protein (p.Arg169Gln). This variant is present in population databases (rs77563738, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with ADA2-related conditions (PMID: 24552284, 24552285, 25888558, 26867732). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 120303). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ADA2 protein function. Experimental studies have shown that this missense change affects ADA2 function (PMID: 24552285, 26867732). For these reasons, this variant has been classified as Pathogenic.

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

From GeneReviews, SCV000994598.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001448498.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: CECR1 c.506G>A (p.Arg169Gln) results in a conservative amino acid change in the encoded protein sequence. CECR1 is also known as ADA2 in the literature and databases. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00047 in 251456 control chromosomes (gnomAD). c.506G>A has been reported (in both homozygous and compound heterozygous states) in the literature in individuals affected with Polyarteritis Nodosa, Childhoood-Onset (e.g. Elkan_2014, Zhou_2014) and ADA2-deficiency (e.g. VanMontfrans_2016). In many families, the variant was reported to segregate with disease. These data indicate that the variant is very likely to be associated with disease. In functional studies performed in both patient-derived cells and in cells transfected with the variant, c.506G>A resulted in reduced enzymatic activity as well as reduced protein secretion (e.g. VanMontfrans_2016, Elkan_2014). Four ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

From Johns Hopkins Genomics, Johns Hopkins University, SCV001469045.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This ADA2 variant has been identified in numerous patients with ADA2-deficiency in both the compound heterozygous and homozygous state. ADA2 c.506G>A is located within the putative receptor-binding domain and functional studies have demonstrated that this variant causes severely decreased levels of secreted ADA2. This variant has been seen in trans with a second disease-causing ADA2 variant in affected individuals within a family. ADA2 c.506G>A (rs77563738) is present in a large population dataset (gnomAD: 134/282860 total alleles; 0.05%; no homozygotes) and has been reported in ClinVar. Three bioinformatic tools queried predict that this substitution would be damaging, and the arginine residue at this position is highly evolutionarily conserved across most species assessed. We consider this variant to be pathogenic.

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

From Genomics England Pilot Project, Genomics England, SCV001760481.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Centogene AG - the Rare Disease Company, SCV002059413.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV003836134.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV005326547.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024