PRKACA p.Phe55=
c.165C>T · rs776568028 · VCV743261
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.12%, amr)
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 -2.3 | |
| Overall | ||
| CADD | 8.951 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
Admixed American · 72/60,004 alleles
Filtering AF
0.0977%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0895%
Overall
0.00539%
87/1,614,060 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.12% | 833 |
| East Asian | 0.0111% | 8,974 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| African / African-American | 0.00133% | 74,934 |
| European (non-Finnish) | 0.000593% | 168,576 |
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
- PRKACA
- Protein
- p.Phe55=
- Coding
- c.165C>T
- MANE Select
- NM_002730
- dbSNP
- rs776568028
- Type
- single nucleotide variant
- Location
- chr19:14106832 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 95.92 · 54 PDB
- Residue 55
- the protein kinase domain; a β-strand; a binding site
Similar variants
- PRKACA p.Gly137Arg Pathogenic/Likely pathogenic ★★ same type
- PRKACA p.Arg271Trp Uncertain significance ★★ ⚠ same type
- PRKACA p.Asn341Ser Uncertain significance ★★ ⚠ same type
- PRKACA p.Gly67Arg Uncertain significance ★★ ⚠ same type
- PRKACA c.109-6C>T Benign/Likely benign ★★ same type
- PRKACA c.47-418C>T Benign/Likely benign ★★ same type
- PRKACA p.Arg281= Benign ★★ same type
- PRKACA p.Gly127= Benign ★★ same type
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/prkaca-p-phe55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown