# NM_002230.4(JUP):c.498G>A (p.Val166=)

https://sugi.bio/variant/jup-p-val166

## Summary

**JUP p.Val166= (c.498G>A)** is classified **Likely benign** in JUP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-25). Very rare (popmax 8.47e-05%, nfe); Associated with Cardiovascular phenotype.

**At a glance:** Likely benign · review: Single submitter · 1 submitter · 1 linked condition · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the JUP gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to Cardiovascular phenotype.

*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 | [JUP](https://sugi.bio/atlas/gene/JUP/) |
| Protein change (HGVS p.) | p.Val166= |
| Coding change (HGVS c.) | c.498G>A |
| MANE Select transcript | [NM_002230](https://www.ncbi.nlm.nih.gov/nuccore/NM_002230) |
| Variant type | single nucleotide variant |
| Location | chr17:41769178-41769178 (GRCh38) |
| ClinVar | [VCV3287292](https://www.ncbi.nlm.nih.gov/clinvar/variation/3287292/) |

**All HGVS expressions:** `LRG_401:g.22535G>A`, `LRG_401t1:c.498G>A`, `LRG_401t2:c.498G>A`, `NC_000017.10:g.39925430C>T`, `NC_000017.11:g.41769178C>T`, `NG_009090.2:g.22535G>A`, `NM_001352773.2:c.498G>A`, `NM_001352774.2:c.498G>A`, `NM_001352775.2:c.498G>A`, `NM_001352776.2:c.498G>A`, `NM_001352777.2:c.498G>A`, `NM_002230.4:c.498G>A`, `NM_021991.4:c.498G>A`

## 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 0.603, GERP -4.69, phastCons 0.998 — weakly conserved position
- CADD: **PHRED 8.825**. 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 **8.47e-05%** (nfe) · 1/1,179,944 in the highest group · 1/1,602,636 alleles overall — very rare (popmax 8.47e-05%, 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}

**JUP** population constraint: LOEUF 0.533, pLI 0.74487, missense-Z 2.0603. *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 **166** lies in the 'interaction with dsc1 and dsg1' region; an α-helix.

AlphaFold model confidence (whole protein): pLDDT 80.88, 64% of residues very-high.

**1 experimental structure(s)** (PDB): [3IFQ](https://www.rcsb.org/structure/3IFQ).

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

*Describes the biological roles of JUP (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:** JUP's established molecular role includes transcription coactivator activity. p.Val166= falls in the interaction with dsc1 and dsg1 region.


### Pathways affected {#pathways}

JUP participates in **20 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Adherens junctions interactions](https://reactome.org/content/detail/R-HSA-418990) | curated |
| [CDC42 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013148) | curated |
| [Degradation of CDH1](https://reactome.org/content/detail/R-HSA-9766229) | curated |
| [Formation of the cornified envelope](https://reactome.org/content/detail/R-HSA-6809371) | curated |
| [Keratinization](https://reactome.org/content/detail/R-HSA-6805567) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [RHOA GTPase cycle](https://reactome.org/content/detail/R-HSA-8980692) | curated |
| [RHOB GTPase cycle](https://reactome.org/content/detail/R-HSA-9013026) | curated |
| [RHOC GTPase cycle](https://reactome.org/content/detail/R-HSA-9013106) | curated |
| [RHOH GTPase cycle](https://reactome.org/content/detail/R-HSA-9013407) | curated |
| [RHOJ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013409) | curated |
| [RHOQ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013406) | curated |
| [Regulation of CDH1 Function](https://reactome.org/content/detail/R-HSA-9764561) | curated |
| [Regulation of CDH1 posttranslational processing and trafficking to plasma membrane](https://reactome.org/content/detail/R-HSA-9768727) | curated |
| [VEGFR2 mediated vascular permeability](https://reactome.org/content/detail/R-HSA-5218920) | curated |
| [Activation of STAT3 by cadherin engagement](https://reactome.org/content/detail/R-HSA-9958825) | electronic |
| [CDH11 homotypic and heterotypic interactions](https://reactome.org/content/detail/R-HSA-9833576) | electronic |
| [Regulation of CDH11 function](https://reactome.org/content/detail/R-HSA-9762292) | electronic |
| [Regulation of CDH19 Expression and Function](https://reactome.org/content/detail/R-HSA-9764302) | electronic |
| [SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST)](https://reactome.org/content/detail/R-HSA-9958810) | electronic |

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

**Molecular function:** transcription coactivator activity, protein phosphatase binding, alpha-catenin binding, cadherin binding, cell adhesion molecule binding, cytoskeletal protein-membrane anchor activity.

**Biological process:** positive regulation of cell-matrix adhesion, desmosome assembly, cell migration, regulation of cell population proliferation, positive regulation of protein import into nucleus, negative regulation of blood vessel endothelial cell migration.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-04-25.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-04-25 |

## Associated conditions {#conditions}

[Cardiovascular phenotype](https://sugi.bio/atlas/disease/cardiovascular-phenotype/).

**Reported phenotype names (ClinVar):** Cardiovascular phenotype.

## Similar variants {#similar}

Related JUP variant pages (same residue, condition, or type): [JUP c.468+4T>C](/variant/jup-c-468-plus-4t-c), [JUP c.707+5C>A](/variant/jup-c-707-plus-5c-a), [JUP c.-1G>A](/variant/jup-c-minus-1g-a), [JUP p.Ala178Val](/variant/jup-p-ala178val), [JUP p.Ala263Val](/variant/jup-p-ala263val), [JUP p.Ala314Gly](/variant/jup-p-ala314gly), [JUP p.Ala347Val](/variant/jup-p-ala347val), [JUP p.Ala516Asp](/variant/jup-p-ala516asp).

### 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 3287292). 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.*