# NM_016592.5(GNAS):c.409C>T (p.Pro137Ser)

https://sugi.bio/variant/gnas-p-pro137ser

## Summary

**GNAS p.Pro137Ser (c.409C>T)** is classified **Uncertain significance** in GNAS (ClinVar, Single submitter, 1 submitter; last evaluated 2014-07-24). Very rare (popmax 0.0011%, sas); Associated with Inborn genetic diseases.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs779401973 · 1 submitter · 1 linked condition · very rare (popmax 0.0011%, sas)

## For patients & families {#patients}

This is a change in the GNAS gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to Inborn genetic diseases.

*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 | [GNAS](https://sugi.bio/atlas/gene/GNAS/) |
| Protein change (HGVS p.) | p.Pro137Ser |
| Coding change (HGVS c.) | c.409C>T |
| MANE Select transcript | [NM_000516](https://www.ncbi.nlm.nih.gov/nuccore/NM_000516) (variant reported on NM_016592) |
| dbSNP | [rs779401973](https://www.ncbi.nlm.nih.gov/snp/rs779401973/) |
| Variant type | single nucleotide variant |
| Location | chr20:58840515-58840515 (GRCh38) |
| ClinVar | [VCV520563](https://www.ncbi.nlm.nih.gov/clinvar/variation/520563/) |

**All HGVS expressions:** `LRG_1051:g.15389G>A`, `NC_000020.10:g.57415570C>T`, `NC_000020.11:g.58840515C>T`, `NG_016194.2:g.5776C>T`, `NG_021433.1:g.15389G>A`, `NM_001410912.1:c.-329C>T`, `NM_016592.5:c.409C>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 5.268, GERP 0.452, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 23.2**. 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.*
- 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 **0.0011%** (sas) · 1/91,080 in the highest group · 2/1,613,578 alleles overall — very rare (popmax 0.0011%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.0011% | 91,080 |
| European (non-Finnish) | 8.47e-05% | 1,179,998 |

*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}

**GNAS** population constraint: LOEUF 0.302, pLI 0.99999, missense-Z 4.8425; ClinGen dosage — haploinsufficiency 3/3, triplosensitivity 0/3. *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 **137** lies in the 'disordered' region; the g-alpha domain.

AlphaFold model confidence (whole protein): pLDDT 59.47, 4% of residues very-high.

**200 experimental structure(s)** (PDB): [24TB](https://www.rcsb.org/structure/24TB), [24TI](https://www.rcsb.org/structure/24TI), [25NV](https://www.rcsb.org/structure/25NV), [25NX](https://www.rcsb.org/structure/25NX), [5G53](https://www.rcsb.org/structure/5G53), [5UZ7](https://www.rcsb.org/structure/5UZ7) — incl. mutant structure 6AU6.

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

*Describes the biological roles of GNAS (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:** GNAS's established molecular role includes G protein activity. p.Pro137Ser falls in the disordered region. In Reactome, GNAS is annotated in disease pathway(s) including **ADORA2B mediated anti-inflammatory cytokines production**.

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

### Pathways affected {#pathways}

GNAS participates in **13 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [ADORA2B mediated anti-inflammatory cytokines production](https://reactome.org/content/detail/R-HSA-9660821) | electronic |
| [Glucagon signaling in metabolic regulation](https://reactome.org/content/detail/R-HSA-163359) | curated |
| [Glucagon-type ligand receptors](https://reactome.org/content/detail/R-HSA-420092) | curated |
| [Hedgehog 'off' state](https://reactome.org/content/detail/R-HSA-5610787) | curated |
| [High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells](https://reactome.org/content/detail/R-HSA-9856530) | curated |
| [PKA activation in glucagon signalling](https://reactome.org/content/detail/R-HSA-164378) | curated |
| [Vasopressin regulates renal water homeostasis via Aquaporins](https://reactome.org/content/detail/R-HSA-432040) | curated |
| [G alpha (i) signalling events](https://reactome.org/content/detail/R-HSA-418594) | electronic |
| [G alpha (s) signalling events](https://reactome.org/content/detail/R-HSA-418555) | electronic |
| [G alpha (z) signalling events](https://reactome.org/content/detail/R-HSA-418597) | electronic |
| [GPER1 signaling](https://reactome.org/content/detail/R-HSA-9634597) | electronic |
| [Glucagon-like Peptide-1 (GLP1) regulates insulin secretion](https://reactome.org/content/detail/R-HSA-381676) | electronic |
| [Prostacyclin signalling through prostacyclin receptor](https://reactome.org/content/detail/R-HSA-392851) | electronic |

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

**Molecular function:** G protein activity, D1 dopamine receptor binding.

**Biological process:** response to parathyroid hormone, intracellular glucose homeostasis, adenylate cyclase-activating G protein-coupled receptor signaling pathway, adenylate cyclase-activating serotonin receptor signaling pathway, regulation of skeletal muscle contraction, response to prostaglandin E.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2014-07-24.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2014-07-24 |

## Associated conditions {#conditions}

[Inborn genetic diseases](https://sugi.bio/atlas/disease/inborn-genetic-diseases/).

**Reported phenotype names (ClinVar):** Inborn genetic diseases.

## Similar variants {#similar}

Related GNAS variant pages (same residue, condition, or type): [GNAS p.Pro137Leu](/variant/gnas-p-pro137leu), [GNAS p.Val137=](/variant/gnas-p-val137), [GNAS p.Val137Gly](/variant/gnas-p-val137gly), [GNAS c.432+1G>A](/variant/gnas-c-432-plus-1g-a), [GNAS p.Arg265Cys](/variant/gnas-p-arg265cys), [GNAS p.Arg385His](/variant/gnas-p-arg385his), [GNAS p.Arg42Cys](/variant/gnas-p-arg42cys), [GNAS p.Arg385Cys](/variant/gnas-p-arg385cys).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 520563). 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.*