Is PRKAR1A p.Pro288= (c.864A>G) pathogenic?

PRKAR1A p.Pro288= (c.864A>G) is classified Likely benign in PRKAR1A (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-05). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PRKAR1A p.Pro288= (c.864A>G)?

PRKAR1A p.Pro288= (c.864A>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PRKAR1A p.Pro288= (c.864A>G) in the general population?

PRKAR1A p.Pro288= (c.864A>G) is absent from gnomAD v4.1 (gnomAD).

PRKAR1A p.Pro288=

c.864A>G · rs2509438039 · VCV1764151

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 -0.91	GERP -4.3
Overall
CADD	7.455	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PRKAR1A
Protein: p.Pro288=
Coding: c.864A>G
MANE Select: NM_002734
dbSNP: rs2509438039
Type: single nucleotide variant
Location: chr17:68528964 (GRCh38)
Gene constraint: LOEUF 0.158 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.95 · 3 PDB

Full PRKAR1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRKAR1A p.Pro288Ala Uncertain significance ★★ ⚠ same residue
PRKAR1A p.Pro288Ser 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.Arg16Ter 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-pro288 (accessed [today's date]).

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