The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000022.4(ADA):c.603C>G (p.Tyr201Ter)

CA409120740

555182 (ClinVar)

Gene: ADA
Condition: adenosine deaminase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 3d3dd172-f31e-4e3e-b101-075568b4d23a

HGVS expressions

NM_000022.4:c.603C>G
NM_000022.4(ADA):c.603C>G (p.Tyr201Ter)
NC_000020.11:g.44624205G>C
CM000682.2:g.44624205G>C
NC_000020.10:g.43252846G>C
CM000682.1:g.43252846G>C
NC_000020.9:g.42686260G>C
NG_007385.1:g.32531C>G
ENST00000372874.9:c.603C>G
ENST00000372874.8:c.603C>G
ENST00000372887.5:c.*229G>C
ENST00000464097.5:n.277C>G
ENST00000492931.5:n.687C>G
ENST00000536532.5:c.603C>G
ENST00000537820.1:c.603C>G
ENST00000539235.5:c.219-1127C>G
NM_000022.2:c.603C>G
NM_000022.3:c.603C>G
NM_001322050.1:c.198C>G
NM_001322051.1:c.603C>G
NR_136160.1:n.754C>G
NM_001322050.2:c.198C>G
NM_001322051.2:c.603C>G
NR_136160.2:n.695C>G

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ADA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
The c.603C>G (p.Tyr201Ter) (NM_000022.4) variant in ADA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 6/12 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1_Met). The highest population minor allele frequency in gnomAD v4 is 0.00002992 (1/33422 alleles) in African/African American population, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). There are no publications for this variant in the literature. Patient # 46 was found to be heterozygous for c.603C>G (p.Tyr201*) and c.632G>A (p.Arg211His) which is classified as pathogenic for SCID by the ClinGen SCID VCEP (1 pt.) (PMID: 26255240, PM3). In summary, this variant meets the criteria to be classified as a Pathogenic variant for autosomal recessive severe combined immunodeficiency due to ADA deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PM2_supporting,PM3,PVS1 (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v4 is 0.00002992 (1/33422 alleles) in African/African American population, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). There are no publications for this variant in the literature.
PVS1
The c.603C>G (p.Tyr201Ter) (NM_000022.4) variant in ADA is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 6/12 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1 Met).
PM3
Patient # 46 was found to be heterozygous for c.603C>G (p.Tyr201*) and c.632G>A (p.Arg211His) which is classified as pathogenic for SCID by the ClinGen SCID VCEP (1 pt.) (PMID: 26255240, PM3)
Approved on: 2024-01-24
Published on: 2024-01-24
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