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NM_000022.4(ADA):c.890C>A (p.Pro297Gln) AND ADA-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 4, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004752679.1

Allele description [Variation Report for NM_000022.4(ADA):c.890C>A (p.Pro297Gln)]

NM_000022.4(ADA):c.890C>A (p.Pro297Gln)

Gene:
ADA:adenosine deaminase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.12
Genomic location:
Preferred name:
NM_000022.4(ADA):c.890C>A (p.Pro297Gln)
HGVS:
  • NC_000020.11:g.44621103G>T
  • NG_007385.1:g.35633C>A
  • NM_000022.3:c.890C>A
  • NM_000022.4:c.890C>AMANE SELECT
  • NM_001322050.2:c.485C>A
  • NM_001322051.2:c.818C>A
  • NP_000013.2:p.Pro297Gln
  • NP_001308979.1:p.Pro162Gln
  • NP_001308980.1:p.Pro273Gln
  • LRG_16t1:c.890C>A
  • LRG_16:g.35633C>A
  • NC_000020.10:g.43249744G>T
  • NM_000022.2:c.890C>A
  • NM_000022.4:c.890C>A
  • NR_136160.2:n.917C>A
  • P00813:p.Pro297Gln
Protein change:
P162Q; PRO297GLN
Links:
UniProtKB: P00813#VAR_002238; UniProtKB/Swiss-Prot: VAR_002238; OMIM: 608958.0009; dbSNP: rs121908718
NCBI 1000 Genomes Browser:
rs121908718
Molecular consequence:
  • NM_000022.4:c.890C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322050.2:c.485C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322051.2:c.818C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136160.2:n.917C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
ADA-related disorder
Synonyms:
ADA-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005345691PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Sep 4, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005345691.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The ADA c.890C>A variant is predicted to result in the amino acid substitution p.Pro297Gln. This variant has been reported in the homozygous and compound heterozygous states in individuals with partial adenosine deaminase (ADA) deficiency (Hirschhorn et al. 1989. PubMed ID: 2783588; Hirschhorn et al. 1990. PubMed ID: 2166947). Functional studies suggest that this variant impacts ADA function (Hirschhorn et al. 1989. PubMed ID: 2783588; Hirschhorn et al. 1990. PubMed ID: 2166947). Of note, another variant impacting the same amino acid [c.890C>T (p.Pro297Leu)] was reported in the compound heterozygous state in an individual with predominantly antibody deficiency (Patient P221, Rojas-Restrepo. 2021. PubMed ID: 34975878). The c.890C>A (p.Pro297Gln) variant is reported in 0.020% of alleles in individuals of Latino descent in gnomAD and has conflicting interpretations in ClinVar regarding its pathogenicity, ranging from pathogenic to likely pathogenic to uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/1961/). Taken together, this variant is interpreted as likely pathogenic.

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

Last Updated: Feb 25, 2025