Is ADA2 p.Gly47= (c.141G>A) pathogenic?

ADA2 p.Gly47= (c.141G>A) is classified Likely benign in ADA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). Very rare (popmax 0.00133%, afr); Associated with deficiency of adenosine deaminase 2.

What condition is associated with ADA2 p.Gly47= (c.141G>A)?

ADA2 p.Gly47= (c.141G>A) is associated with deficiency of adenosine deaminase 2 (ClinVar).

How common is ADA2 p.Gly47= (c.141G>A) in the general population?

ADA2 p.Gly47= (c.141G>A) is very rare (popmax 0.00133%, afr) (gnomAD).

How is Deficiency of adenosine deaminase 2 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ADA2 p.Gly47=

c.141G>A · rs764524723 · VCV1651248

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

deficiency of adenosine deaminase 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.2	GERP -3.3
Overall
CADD	0.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,028 alleles

Overall 6.84e-05% 1/1,461,454 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ADA2
Protein: p.Gly47=
Coding: c.141G>A
MANE Select: NM_001166105 · reported on NM_001282225
dbSNP: rs764524723
Type: single nucleotide variant
Location: chr22:17209537 (GRCh38)
Structure: AlphaFold pLDDT 85.04 · 1 PDB

Full ADA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

deficiency of adenosine deaminase 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Deficiency of adenosine deaminase 2 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

ADA2 p.Gly47Ala Pathogenic ★★ ⚠ same residue
ADA2 p.Gly47Arg Pathogenic ★★ same residue
ADA2 p.Gly47Trp Pathogenic ★★ same residue
ADA2 p.Gly47Val Pathogenic/Likely pathogenic ★★ same residue
ADA2 p.Gly47Glu Likely pathogenic ★ same residue
ADA2 c.754-2A>G Likely pathogenic ★★ same condition
ADA2 c.882-2A>G Pathogenic ★★ same condition
ADA2 c.973-2A>G Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ada2-p-gly47 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown