# NM_003995.4(NPR2):c.226T>C (p.Ser76Pro)

https://sugi.bio/variant/npr2-p-ser76pro

## Summary

**NPR2 p.Ser76Pro (c.226T>C)** is classified **Pathogenic** in NPR2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2013-10-01). AlphaMissense: likely pathogenic (0.9778); Absent from gnomAD v4.1; Associated with short stature with nonspecific skeletal abnormalities.

**At a glance:** Pathogenic · review: No assertion criteria · rsID rs796065355 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the NPR2 gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to short stature with nonspecific skeletal abnormalities.

*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 | [NPR2](https://sugi.bio/atlas/gene/NPR2/) |
| Protein change (HGVS p.) | p.Ser76Pro |
| Coding change (HGVS c.) | c.226T>C |
| MANE Select transcript | [NM_003995](https://www.ncbi.nlm.nih.gov/nuccore/NM_003995) |
| dbSNP | [rs796065355](https://www.ncbi.nlm.nih.gov/snp/rs796065355/) |
| Variant type | single nucleotide variant |
| Location | chr9:35792634-35792634 (GRCh38) |
| ClinVar | [VCV208357](https://www.ncbi.nlm.nih.gov/clinvar/variation/208357/) |

**All HGVS expressions:** `NC_000009.11:g.35792631T>C`, `NC_000009.12:g.35792634T>C`, `NG_009249.1:g.5226T>C`, `NM_001378923.1:c.226T>C`, `NM_003995.4:c.226T>C`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9778) — concordant with the pathogenic call
- REVEL 0.567 (indeterminate)
- SaProt LLR -11.819 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this damaging; REVEL is indeterminate
- Conservation: phyloP 7.932, GERP 1.73, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 28.3**. 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**NPR2** population constraint: LOEUF 0.517, pLI 0.44949, missense-Z 4.5979. *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 **76** lies in a UniProt-annotated variant site (in snsk1; loss of c-type natriuretic peptide-induced signaling; dominant negative effect; loss of localization to the plasma membrane).

AlphaFold model confidence (whole protein): pLDDT 84.00, 45% of residues very-high.

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

*Describes the biological roles of NPR2 (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:** NPR2's established molecular role includes guanylate cyclase activity.


### Pathways affected {#pathways}

NPR2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Physiological factors](https://reactome.org/content/detail/R-HSA-5578768) | curated |

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

**Molecular function:** guanylate cyclase activity, natriuretic peptide receptor activity, peptide hormone binding, hormone binding.

**Biological process:** cGMP biosynthetic process, receptor guanylyl cyclase signaling pathway, cellular response to granulocyte macrophage colony-stimulating factor stimulus.

## Clinical significance {#significance}

**Pathogenic** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2013-10-01.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| OMIM | Pathogenic | no assertion criteria provided | literature only | 2013-10-01 |

## Associated conditions {#conditions}

[short stature with nonspecific skeletal abnormalities](https://sugi.bio/atlas/disease/short-stature-with-nonspecific-skeletal-abnormalities/).

**Reported phenotype names (ClinVar):** Short stature with nonspecific skeletal abnormalities.

## Similar variants {#similar}

Related NPR2 variant pages (same residue, condition, or type): [NPR2 p.Arg479Ter](/variant/npr2-p-arg479ter), [NPR2 p.Arg767Ter](/variant/npr2-p-arg767ter), [NPR2 p.Gln201Ter](/variant/npr2-p-gln201ter), [NPR2 p.Ala511=](/variant/npr2-p-ala511), [NPR2 p.Arg165His](/variant/npr2-p-arg165his), [NPR2 p.Arg358Trp](/variant/npr2-p-arg358trp), [NPR2 p.Arg495His](/variant/npr2-p-arg495his), [NPR2 p.Arg557His](/variant/npr2-p-arg557his).

### 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 208357). 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.*