# NM_006258.4(PRKG1):c.307C>T (p.Pro103Ser)

https://sugi.bio/variant/prkg1-p-pro103ser

## Summary

**PRKG1 p.Pro103Ser (c.307C>T)** is classified **Uncertain significance** in PRKG1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-01-22). Very rare (popmax 0.00102%, nfe); Associated with aortic aneurysm, familial thoracic 8.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs201361942 · 2 submitters · 2 linked conditions · very rare (popmax 0.00102%, nfe)

## For patients & families {#patients}

This is a change in the PRKG1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to aortic aneurysm, familial thoracic 8.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant |
| Age of onset (of this condition) | Adolescent, Adult, Childhood |
| Diagnostic panels | PRKG1 is a diagnostic-grade gene on 2 Genomics England panels |

**Commonly reported features of Familial thoracic aortic aneurysm and aortic dissection** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Cutis marmorata — Very frequent (99-80%)
- Abnormality of connective tissue — Very frequent (99-80%)
- Cystic medial necrosis of the aorta — Very frequent (99-80%)
- Abnormality iris morphology — Frequent (79-30%)
- Hypertension — Frequent (79-30%)
- Cardiomegaly — Frequent (79-30%)
- Aortic regurgitation — Frequent (79-30%)
- Coronaryartery atherosclerosis — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015966/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PRKG1](https://sugi.bio/atlas/gene/PRKG1/) |
| Protein change (HGVS p.) | p.Pro103Ser |
| Coding change (HGVS c.) | c.307C>T |
| MANE Select transcript | [NM_006258](https://www.ncbi.nlm.nih.gov/nuccore/NM_006258) |
| dbSNP | [rs201361942](https://www.ncbi.nlm.nih.gov/snp/rs201361942/) |
| Variant type | single nucleotide variant |
| Location | chr10:51074897-51074897 (GRCh38) |
| ClinVar | [VCV2098464](https://www.ncbi.nlm.nih.gov/clinvar/variation/2098464/) |

**All HGVS expressions:** `LRG_1135:g.88747C>T`, `LRG_1135t1:c.307C>T`, `LRG_1135t2:c.267-78267C>T`, `NC_000010.10:g.52834657C>T`, `NC_000010.11:g.51074897C>T`, `NG_029982.1:g.88747C>T`, `NM_001098512.3:c.267-78267C>T`, `NM_001374782.1:c.307C>T`, `NM_006258.3:c.307C>T`, `NM_006258.4:c.307C>T`

## 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 5.976, GERP 2.58, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 21.2**. 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.*
- Regional missense constraint: **o/e 0.71** across the covering region of the MANE Select transcript (51,074,712–52,280,863), spanning 1,206,151 bp. Chi-square p 7e-12. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00102%** (nfe) · FAF95 0.000545% · FAF99 0.000431% · 12/1,173,122 in the highest group · 12/1,604,040 alleles overall — very rare (popmax 0.00102%, nfe).

*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}

**PRKG1** population constraint: LOEUF 0.534, pLI 0.663, missense-Z 3.881. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **familial thoracic aortic aneurysm and aortic dissection** — Strong (AD)

## Protein context {#protein}

Residue **103** lies in a turn; the 'cgmp-binding, high affinity' region.

AlphaFold model confidence (whole protein): pLDDT 86.87, 55% of residues very-high.

**26 experimental structure(s)** (PDB): [1ZXA](https://www.rcsb.org/structure/1ZXA), [3NMD](https://www.rcsb.org/structure/3NMD), [3OCP](https://www.rcsb.org/structure/3OCP), [3OD0](https://www.rcsb.org/structure/3OD0), [3OGJ](https://www.rcsb.org/structure/3OGJ), [4KU7](https://www.rcsb.org/structure/4KU7).

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

*Describes the biological roles of PRKG1 (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:** PRKG1's established molecular role includes protein kinase activity. p.Pro103Ser falls in the cgmp-binding, high affinity region. In Reactome, PRKG1 is annotated in disease pathway(s) including **Maturation of DENV proteins**.

**Disease mechanism (Reactome):** PRKG1 loss or alteration is curated in [Maturation of DENV proteins](https://reactome.org/content/detail/R-HSA-9918432).

### Pathways affected {#pathways}

PRKG1 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Maturation of DENV proteins](https://reactome.org/content/detail/R-HSA-9918432) | other |
| [Ca2+ pathway](https://reactome.org/content/detail/R-HSA-4086398) | electronic |
| [Rap1 signalling](https://reactome.org/content/detail/R-HSA-392517) | other |
| [cGMP effects](https://reactome.org/content/detail/R-HSA-418457) | other |

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

**Molecular function:** protein kinase activity, cGMP-dependent protein kinase activity, calcium channel regulator activity, identical protein binding.

**Biological process:** regulation of vascular permeability, relaxation of vascular associated smooth muscle, negative regulation of platelet aggregation, negative regulation of vascular associated smooth muscle cell proliferation, negative regulation of vascular associated smooth muscle cell migration.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2023-01-22.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2022–2023); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-09-16 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-01-22 |

## Associated conditions {#conditions}

[aortic aneurysm, familial thoracic 8](https://sugi.bio/atlas/disease/aortic-aneurysm-familial-thoracic-8/), [familial thoracic aortic aneurysm and aortic dissection](https://sugi.bio/atlas/disease/familial-thoracic-aortic-aneurysm-and-aortic-dissection/).

**Reported phenotype names (ClinVar):** Aortic aneurysm, familial thoracic 8, Familial thoracic aortic aneurysm and aortic dissection, Thoracic aortic aneurysms and dissections.

## Similar variants {#similar}

Related PRKG1 variant pages (same residue, condition, or type): [PRKG1 p.Arg192Gln](/variant/prkg1-p-arg192gln), [PRKG1 c.1001+3A>G](/variant/prkg1-c-1001-plus-3a-g), [PRKG1 c.1832+5G>A](/variant/prkg1-c-1832-plus-5g-a), [PRKG1 c.478+4C>T](/variant/prkg1-c-478-plus-4c-t), [PRKG1 c.478+5G>A](/variant/prkg1-c-478-plus-5g-a), [PRKG1 c.840+5G>T](/variant/prkg1-c-840-plus-5g-t), [PRKG1 c.935+5G>A](/variant/prkg1-c-935-plus-5g-a), [PRKG1 p.Ala356Val](/variant/prkg1-p-ala356val).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2098464). 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.*