# NM_002736.3(PRKAR2B):c.888A>G (p.Val296=)

https://sugi.bio/variant/prkar2b-p-val296

## Summary

**PRKAR2B p.Val296= (c.888A>G)** is classified **Benign** in PRKAR2B (ClinVar, Single submitter, 1 submitter; last evaluated 2017-08-02). Rare (popmax 0.362%, afr).

**At a glance:** Benign · review: Single submitter · rsID rs77265974 · 1 submitter · rare (popmax 0.362%, afr)

## For patients & families {#patients}

This is a change in the PRKAR2B gene that is classified as benign — not considered disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PRKAR2B](https://sugi.bio/atlas/gene/PRKAR2B/) |
| Protein change (HGVS p.) | p.Val296= |
| Coding change (HGVS c.) | c.888A>G |
| MANE Select transcript | [NM_002736](https://www.ncbi.nlm.nih.gov/nuccore/NM_002736) |
| dbSNP | [rs77265974](https://www.ncbi.nlm.nih.gov/snp/rs77265974/) |
| Variant type | single nucleotide variant |
| Location | chr7:107153221-107153221 (GRCh38) |
| ClinVar | [VCV782271](https://www.ncbi.nlm.nih.gov/clinvar/variation/782271/) |

**All HGVS expressions:** `NC_000007.13:g.106793666A>G`, `NC_000007.14:g.107153221A>G`, `NM_002736.3:c.888A>G`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.776, GERP -5.86, phastCons 0.986 — weakly conserved position
- CADD: **PHRED 5.274**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PRKAR2B (811 scored positions, the nearest 30 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **0.362%** (afr) · FAF95 0.327% · FAF99 0.313% · 271/74,858 in the highest group · 315/1,609,514 alleles overall — rare (popmax 0.362%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.362% | 276 |
| Admixed American | 0.0403% | 2,481 |
| Middle Eastern | 0.0331% | 3,021 |
| Remaining individuals (not grpmax-eligible) | 0.0225% | 4,452 |
| South Asian | 0.00111% | 89,974 |
| European (non-Finnish) | 0.000255% | 392,623 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**PRKAR2B** population constraint: LOEUF 0.658, pLI 0.54152, missense-Z 0.97873. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **296** lies in a binding site.

AlphaFold model confidence (whole protein): pLDDT 79.37, 42% of residues very-high.

## What this gene does {#gene-function}

*Describes the biological roles of PRKAR2B (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** PRKAR2B's established molecular role includes cAMP-dependent protein kinase inhibitor activity. In Reactome, PRKAR2B is annotated in disease pathway(s) including **ADORA2B mediated anti-inflammatory cytokines production**, **FCGR3A-mediated IL10 synthesis**.

**Disease mechanism (Reactome):** PRKAR2B loss or alteration is curated in [ADORA2B mediated anti-inflammatory cytokines production](https://reactome.org/content/detail/R-HSA-9660821), [FCGR3A-mediated IL10 synthesis](https://reactome.org/content/detail/R-HSA-9664323).

### Pathways affected {#pathways}

PRKAR2B participates in **19 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [ADORA2B mediated anti-inflammatory cytokines production](https://reactome.org/content/detail/R-HSA-9660821) | other |
| ⚕ [FCGR3A-mediated IL10 synthesis](https://reactome.org/content/detail/R-HSA-9664323) | other |
| [CREB1 phosphorylation through the activation of Adenylate Cyclase](https://reactome.org/content/detail/R-HSA-442720) | curated |
| [DARPP-32 events](https://reactome.org/content/detail/R-HSA-180024) | curated |
| [Hedgehog 'off' state](https://reactome.org/content/detail/R-HSA-5610787) | curated |
| [Loss of Nlp from mitotic centrosomes](https://reactome.org/content/detail/R-HSA-380259) | curated |
| [Loss of proteins required for interphase microtubule organization from the centrosome](https://reactome.org/content/detail/R-HSA-380284) | curated |
| [PKA activation](https://reactome.org/content/detail/R-HSA-163615) | curated |
| [PKA activation in glucagon signalling](https://reactome.org/content/detail/R-HSA-164378) | curated |
| [Recruitment of NuMA to mitotic centrosomes](https://reactome.org/content/detail/R-HSA-380320) | curated |
| [Recruitment of mitotic centrosome proteins and complexes](https://reactome.org/content/detail/R-HSA-380270) | curated |
| [Regulation of PLK1 Activity at G2/M Transition](https://reactome.org/content/detail/R-HSA-2565942) | curated |
| [Vasopressin regulates renal water homeostasis via Aquaporins](https://reactome.org/content/detail/R-HSA-432040) | curated |
| [AURKA Activation by TPX2](https://reactome.org/content/detail/R-HSA-8854518) | other |
| [Anchoring of the basal body to the plasma membrane](https://reactome.org/content/detail/R-HSA-5620912) | other |
| [Factors involved in megakaryocyte development and platelet production](https://reactome.org/content/detail/R-HSA-983231) | other |
| [GPER1 signaling](https://reactome.org/content/detail/R-HSA-9634597) | other |
| [Glucagon-like Peptide-1 (GLP1) regulates insulin secretion](https://reactome.org/content/detail/R-HSA-381676) | electronic |
| [High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells](https://reactome.org/content/detail/R-HSA-9856530) | other |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** cAMP-dependent protein kinase inhibitor activity, cAMP-dependent protein kinase regulator activity, ubiquitin protein ligase binding, protein kinase A catalytic subunit binding.

**Biological process:** negative regulation of cAMP/PKA signal transduction.

## Clinical significance {#significance}

**Benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2017-08-02.

**Submitter consensus:** unanimous (1/1 Benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2017-08-02 |

**Reported phenotype names (ClinVar):** not provided, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM, none provided.

## Similar variants {#similar}

Related PRKAR2B variant pages (same residue, condition, or type): [PRKAR2B p.Val296Leu](/variant/prkar2b-p-val296leu), [PRKAR2B p.Ile396=](/variant/prkar2b-p-ile396), [PRKAR2B c.307+1G>A](/variant/prkar2b-c-307-plus-1g-a), [PRKAR2B p.Arg218His](/variant/prkar2b-p-arg218his), [PRKAR2B p.Asn143Tyr](/variant/prkar2b-p-asn143tyr), [PRKAR2B p.Asn229Asp](/variant/prkar2b-p-asn229asp), [PRKAR2B p.Asn229Ser](/variant/prkar2b-p-asn229ser), [PRKAR2B p.Asn75Ser](/variant/prkar2b-p-asn75ser).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 782271). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*