PRKAR1A p.Ser193=
c.579T>C · rs2143322046 · VCV1106313
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
2
hereditary neoplastic syndrome
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 -0.024 | GERP -3, phastCons 0.92 |
| Overall | ||
| CADD | 9.584 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,752 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,506 alleles · very rare
exomes 2/1,461,748 · genomes 0/151,758 · 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.Ser193=
- Coding
- c.579T>C
- MANE Select
- NM_002734
- dbSNP
- rs2143322046
- Type
- single nucleotide variant
- Location
- chr17:68525783 (GRCh38)
- Gene constraint
- LOEUF 0.158 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.95 · 3 PDB
Similar variants
- PRKAR1A p.Ser193Asn Uncertain significance ★★ ⚠ same residue
- PRKAR1A p.Ser193Gly Uncertain significance ★★ ⚠ same residue
- PRKAR1A p.Ser193Arg Uncertain significance ★ same residue
- PRKAR1A c.502+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PRKAR1A c.549+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PRKAR1A c.891+1G>A Likely pathogenic ★★ same condition
- PRKAR1A c.891+3A>G Likely pathogenic ★★ same condition
- PRKAR1A c.892-2A>G Pathogenic/Likely 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-ser193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown