Is PRKAR1A p.Pro320= (c.960T>G) pathogenic?

PRKAR1A p.Pro320= (c.960T>G) is classified Likely benign in PRKAR1A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-07-14). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PRKAR1A p.Pro320= (c.960T>G)?

PRKAR1A p.Pro320= (c.960T>G) is associated with hereditary neoplastic syndrome, Carney complex, type 1 (ClinVar).

How common is PRKAR1A p.Pro320= (c.960T>G) in the general population?

PRKAR1A p.Pro320= (c.960T>G) is absent from gnomAD v4.1 (gnomAD).

PRKAR1A p.Pro320=

c.960T>G · rs2143384159 · VCV1086888

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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 0.17	GERP 1, phastCons 0.99
Overall
CADD	11.36	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.Pro320=
Coding: c.960T>G
MANE Select: NM_002734
dbSNP: rs2143384159
Type: single nucleotide variant
Location: chr17:68529988 (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

Also linked: Carney complex, type 1

Similar variants

PRKAR1A p.Pro320Leu Uncertain significance ★★ ⚠ same residue
PRKAR1A p.Pro320Ser Uncertain significance ★ ⚠ same residue
PRKAR1A p.Pro320Thr Uncertain significance ★ ⚠ same residue
PRKAR1A p.Pro320fs Pathogenic ★★ 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

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-pro320 (accessed [today's date]).

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