PRKAR1A p.Arg16=
c.48A>C · VCV3425067
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 14.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,613,642 alleles · very rare
exomes 1/1,461,314 · genomes 0/152,328 · joint denominator
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
- PRKAR1A
- Protein
- p.Arg16=
- Coding
- c.48A>C
- MANE Select
- NM_002734
- Type
- single nucleotide variant
- Location
- chr17:68515447 (GRCh38)
- Gene constraint
- LOEUF 0.158 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.95 · 3 PDB
- Residue 16
- the 'dimerization and phosphorylation' region
Similar variants
- PRKAR1A p.Arg16Ter Pathogenic ★★ same residue
- PRKAR1A p.Arg16Gln Uncertain significance ★★ ⚠ same residue
- PRKAR1A p.Arg16Gly Uncertain significance ★★ ⚠ same residue
- PRKAR1A c.502+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PRKAR1A c.891+3A>G Likely pathogenic ★★ same condition
- PRKAR1A c.892-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PRKAR1A p.Arg97Ter Pathogenic ★★ same condition
- PRKAR1A p.Met1Val 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/prkar1a-p-arg16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown