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Variant: NM_000022.4(ADA):c.646G>A (p.Gly216Arg)

CA252008

1968 (ClinVar)

Gene: ADA
Condition: adenosine deaminase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: a0ddb75c-ba0b-4900-89fd-00d467cb01d7

HGVS expressions

NM_000022.4:c.646G>A
NM_000022.4(ADA):c.646G>A (p.Gly216Arg)
NC_000020.11:g.44623039C>T
CM000682.2:g.44623039C>T
NC_000020.10:g.43251680C>T
CM000682.1:g.43251680C>T
NC_000020.9:g.42685094C>T
NG_007385.1:g.33697G>A
ENST00000372874.9:c.646G>A
ENST00000372874.8:c.646G>A
ENST00000372887.5:c.152-894C>T
ENST00000464097.5:n.320G>A
ENST00000492931.5:n.730G>A
ENST00000536532.5:c.646G>A
ENST00000537820.1:c.607-109G>A
ENST00000539235.5:c.*30G>A
NM_000022.2:c.646G>A
NM_000022.3:c.646G>A
NM_001322050.1:c.241G>A
NM_001322051.1:c.607-109G>A
NR_136160.1:n.797G>A
NM_001322050.2:c.241G>A
NM_001322051.2:c.607-109G>A
NR_136160.2:n.738G>A

Pathogenic

Met criteria codes 5
PM2_Supporting PP4_Moderate PP1_Strong PM3_Strong PS3_Moderate
Not Met criteria codes 6
BP4 BP1 PS4 PP3 PP2 PM1

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
NM_000022.4 :c.646G>A is a missense variant predicted to cause substitution of Glycine by Arginine at amino acid 216 (p.Gly216Arg). The filtering allele frequency (the upper threshold of the 95% CI of 46/1180026) of the c.646G>A variant in ADA is 0.00002743 for European Non-Finnish chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).The variant has been reported to segregate with SCID in 4 affected family members from 2 families (PP1_strong; PMID : 26255240). This variant has been detected in 15 individuals with ADA deficient SCID. Of those individuals, 3 were compound heterozygous for the variant and a pathogenic variant (Glu319Glyfs*320 ,confirmed in trans ,1pt.). 12 individuals were homozygous for the variant (1 pt.) (total: 2 pts; PM3_Strong ,PMID : 26255240). Male patient with SCID (0.5 pt.), genome sequencing conducted (0.5 pt.), reduced ADA enzyme activity in patient cells (1 pt),SCID phenotype corrected by exogenous ADA supplementation (1 pt.),Increased dATP in pretreatment erythrocytes (2 pts.). (PP4_Moderate (5 pts.), PMID: 1680289). ADA activity in SØ3834 was 30.4 nmol/h/mg protein which is .012 % of wild type ADA activity indicating that this variant impacts protein function (PMID : 9758612, PS3_Moderate). Based on the above evidence, the variant may be classified as pathogenic for autosomal recessive severe combined immunodeficiency due to ADA deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PP1_strong,PM2_supporting,PM3_strong,PP4_moderate,PS3_moderate (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The filtering allele frequency (the upper threshold of the 95% CI of 46/1180026) of the c.646G>A variant in ADA is 0.00002743 for European Non-Finnish chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
PP4_Moderate
Male patient with SCID (0.5 pt), genome sequencing conducted (0.5 pt), reduced ADA enzyme activity in patient cells (1 pt),SCID phenotype corrected by exogenous ADA supplementation (1 pt),Increased dATP in pretreatment erythrocytes (2 pts). (PP4_Moderate (5 pts), PMID: 1680289)
PP1_Strong
The variant has been reported to segregate with SCID in 4 affected family members from 2 families (PP1_strong; PMID : 26255240)
PM3_Strong
This variant has been detected in 15 individuals with ADA deficient SCID. Of those individuals, 3 were compound heterozygous for the variant and a pathogenic variant (Glu319Glyfs*320 ,confirmed in trans ,1pt). 12 individuals were homozygous for the variant (1 pt) (total: 2 pts; PM3_Strong ,PMID : 26255240).
PS3_Moderate
ADA activity in SØ3834 was 30.4 nmol/h/mg protein which is .012 % of wild type ADA activity indicating that this variant impacts protein function (PMID : 9758612, PS3_Moderate).
Not Met criteria codes
BP4
Does not apply.
BP1
Does not apply.
PS4
Does not apply.
PP3
Does not apply.
PP2
Does not apply.
PM1
Does not apply.
Approved on: 2024-01-24
Published on: 2024-01-24
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