PRKAR1B p.Val339=
c.1017C>T · rs149291819 · VCV730568
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.422%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.305 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.8 | GERP -0.45, phastCons 0.003 |
| Overall | ||
| CADD | 5.469 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.422%
African / African-American · 314/74,382 alleles
Filtering AF
0.384%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.369%
Overall
0.0226%
362/1,600,144 alleles · rare
exomes 173/1,447,920 · genomes 189/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.422% | 237 |
| Middle Eastern | 0.0517% | 1,935 |
| East Asian | 0.0269% | 3,721 |
| Remaining individualsnot grpmax-eligible | 0.0243% | 4,112 |
| Admixed American | 0.0226% | 4,415 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00344% | 29,074 |
| South Asian | 0.00223% | 44,796 |
| European (non-Finnish) | 0.00017% | 587,330 |
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
- PRKAR1B
- Protein
- p.Val339=
- Coding
- c.1017C>T
- MANE Select
- NM_001164760
- dbSNP
- rs149291819
- Type
- single nucleotide variant
- Location
- chr7:550559 (GRCh38)
- Gene constraint
- LOEUF 0.686 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.24 · 3 PDB
Similar variants
- PRKAR1B p.Val339Ile Uncertain significance ★ ⚠ same residue
- PRKAR1B p.Arg335Trp Pathogenic/Likely pathogenic ★★ same type
- DNAAF5 p.Asp87Tyr Uncertain significance ★★ ⚠ same type
- DNAAF5 p.Cys138Gly Uncertain significance ★★ ⚠ same type
- DNAAF5 p.Glu8Ala Uncertain significance ★★ ⚠ same type
- DNAAF5 p.Gly150Arg Uncertain significance ★★ ⚠ same type
- DNAAF5 p.Val6Ala Uncertain significance ★★ ⚠ same type
- PRKAR1B p.Ala204Val Uncertain significance ★★ ⚠ 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/prkar1b-p-val339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown