# NM_001839.5(CNN3):c.252G>C (p.Glu84Asp)

https://sugi.bio/variant/cnn3-p-glu84asp

## Summary

**CNN3 p.Glu84Asp (c.252G>C)** is classified **Uncertain significance** in CNN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-06). AlphaMissense: likely pathogenic (0.9777); Very rare (popmax 0.00446%, eas).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely pathogenic · very rare (popmax 0.00446%, eas)

## For patients & families {#patients}

This is a change in the CNN3 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, 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 | [CNN3](https://sugi.bio/atlas/gene/CNN3/) |
| Protein change (HGVS p.) | p.Glu84Asp |
| Coding change (HGVS c.) | c.252G>C |
| MANE Select transcript | [NM_001839](https://www.ncbi.nlm.nih.gov/nuccore/NM_001839) |
| Variant type | single nucleotide variant |
| Location | chr1:94902253-94902253 (GRCh38) |
| ClinVar | [VCV4004306](https://www.ncbi.nlm.nih.gov/clinvar/variation/4004306/) |

**All HGVS expressions:** `NC_000001.10:g.95367809C>G`, `NC_000001.11:g.94902253C>G`, `NM_001286055.2:c.247-468G>C`, `NM_001286056.2:c.129G>C`, `NM_001839.5:c.252G>C`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **damaging** — a triage signal, not a reclassification.

- AlphaMissense **likely pathogenic** (0.9777)
- REVEL 0.409 (indeterminate)
- SaProt LLR -10.65 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this damaging; REVEL makes no call
- Conservation: phyloP 1.425, phastCons 1 — weakly conserved position
- CADD: **PHRED 23.8**. 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 0.66** across the covering region of the MANE Select transcript (94,897,745–94,926,894), spanning 29,149 bp. Chi-square p 8e-12. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>A, Δ0.41 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00446%** (eas) · FAF95 0.000739% · FAF99 0.000276% · 2/44,866 in the highest group · 2/1,457,776 alleles overall — very rare (popmax 0.00446%, eas).

*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}

**CNN3** population constraint: LOEUF 0.43, pLI 0.99878, missense-Z 2.7732. *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 **84** lies in the calponin-homology (ch) domain.

AlphaFold model confidence (whole protein): pLDDT 67.78, 33% of residues very-high.

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

*Describes the biological roles of CNN3 (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:** CNN3's established molecular role includes cadherin binding involved in cell-cell adhesion. p.Glu84Asp falls in the calponin-homology (ch) domain.


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

**Molecular function:** cadherin binding involved in cell-cell adhesion.

**Biological process:** epithelial cell differentiation.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-05-06.

**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 | 2025-05-06 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related CNN3 variant pages (same residue, condition, or type): [CNN3 p.Ala217Thr](/variant/cnn3-p-ala217thr), [CNN3 p.Asn114Ser](/variant/cnn3-p-asn114ser), [CNN3 p.Asn34Ser](/variant/cnn3-p-asn34ser), [CNN3 p.Asp196Gly](/variant/cnn3-p-asp196gly), [CNN3 p.Asp230Asn](/variant/cnn3-p-asp230asn), [CNN3 p.Asp324Asn](/variant/cnn3-p-asp324asn), [CNN3 p.Glu146Asp](/variant/cnn3-p-glu146asp), [CNN3 p.Glu294Asp](/variant/cnn3-p-glu294asp).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); 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 2026-07-14); 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 4004306). 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.*