# NM_024408.4(NOTCH2):c.6415G>T (p.Val2139Phe)

https://sugi.bio/variant/notch2-p-val2139phe

## Summary

**NOTCH2 p.Val2139Phe (c.6415G>T)** is classified **Uncertain significance** in NOTCH2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-04-14). AlphaMissense: likely benign (0.1048); Very rare (popmax 0.000169%, nfe); Associated with Inborn genetic diseases.

**At a glance:** Uncertain significance · review: Multiple submitters · 2 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.000169%, nfe)

## For patients & families {#patients}

This is a change in the NOTCH2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, 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 | [NOTCH2](https://sugi.bio/atlas/gene/NOTCH2/) |
| Protein change (HGVS p.) | p.Val2139Phe |
| Coding change (HGVS c.) | c.6415G>T |
| MANE Select transcript | [NM_024408](https://www.ncbi.nlm.nih.gov/nuccore/NM_024408) |
| Variant type | single nucleotide variant |
| Location | chr1:119916307-119916307 (GRCh38) |
| ClinVar | [VCV4861130](https://www.ncbi.nlm.nih.gov/clinvar/variation/4861130/) |

**All HGVS expressions:** `NC_000001.10:g.120458930C>A`, `NC_000001.11:g.119916307C>A`, `NG_008163.1:g.158347G>T`, `NG_008163.2:g.158355G>T`, `NM_024408.4:c.6415G>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.1048)
- REVEL 0.21 (benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.197 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 7.591, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 22.5**. 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 0.94** across the covering region of the MANE Select transcript (119,915,309–119,916,565), spanning 1,256 bp. Chi-square p 0.14. 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 **0.000169%** (nfe) · FAF95 2.8e-05% · FAF99 1.1e-05% · 2/1,180,026 in the highest group · 2/1,461,892 alleles overall — very rare (popmax 0.000169%, 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}

**NOTCH2** population constraint: LOEUF 0.151, pLI 1, missense-Z 6.0469; ClinGen dosage — haploinsufficiency 0, triplosensitivity 0 (0–3 scale). *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):

- **Alagille syndrome** — Definitive (AD)
- **acroosteolysis dominant type** — Definitive (AD)

## Protein context {#protein}

Residue **2139** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 59.51, 4% of residues very-high.

**2 experimental structure(s)** (PDB): [2OO4](https://www.rcsb.org/structure/2OO4), [5MWB](https://www.rcsb.org/structure/5MWB).

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

*Describes the biological roles of NOTCH2 (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:** NOTCH2's established molecular role includes transcription coactivator activity. p.Val2139Phe falls in the disordered region. In Reactome, NOTCH2 is annotated in disease pathway(s) including **Defective LFNG causes SCDO3**.

**Disease mechanism (Reactome):** NOTCH2 loss or alteration is curated in [Defective LFNG causes SCDO3](https://reactome.org/content/detail/R-HSA-5083630).

### Pathways affected {#pathways}

NOTCH2 participates in **9 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective LFNG causes SCDO3](https://reactome.org/content/detail/R-HSA-5083630) | curated |
| [NOTCH4 Intracellular Domain Regulates Transcription](https://reactome.org/content/detail/R-HSA-9013695) | curated |
| [Notch-HLH transcription pathway](https://reactome.org/content/detail/R-HSA-350054) | curated |
| [Pre-NOTCH Transcription and Translation](https://reactome.org/content/detail/R-HSA-1912408) | curated |
| [Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)](https://reactome.org/content/detail/R-HSA-9976102) | electronic |
| [NOTCH2 Activation and Transmission of Signal to the Nucleus](https://reactome.org/content/detail/R-HSA-2979096) | electronic |
| [NOTCH2 intracellular domain regulates transcription](https://reactome.org/content/detail/R-HSA-2197563) | electronic |
| [Pre-NOTCH Processing in Golgi](https://reactome.org/content/detail/R-HSA-1912420) | electronic |
| [Pre-NOTCH Processing in the Endoplasmic Reticulum](https://reactome.org/content/detail/R-HSA-1912399) | electronic |

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

**Molecular function:** transcription coactivator activity.

**Biological process:** pulmonary valve morphogenesis, Notch signaling pathway, animal organ morphogenesis, negative regulation of gene expression, positive regulation of keratinocyte proliferation, intracellular signal transduction.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-04-14.

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

**Submission history:** 2 submissions (2024–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2026-04-14 |
| Blueprint Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-11-14 |

## Associated conditions {#conditions}

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

**Reported phenotype names (ClinVar):** Inborn genetic diseases, not provided, none provided.

## Similar variants {#similar}

Related NOTCH2 variant pages (same residue, condition, or type): [NOTCH2 p.Arg2003Ter](/variant/notch2-p-arg2003ter), [NOTCH2 p.Ala1416Gly](/variant/notch2-p-ala1416gly), [NOTCH2 p.Arg1231Gln](/variant/notch2-p-arg1231gln), [NOTCH2 p.Arg1231Trp](/variant/notch2-p-arg1231trp), [NOTCH2 p.Arg1718His](/variant/notch2-p-arg1718his), [NOTCH2 p.Arg1801Ser](/variant/notch2-p-arg1801ser), [NOTCH2 p.Arg1824Cys](/variant/notch2-p-arg1824cys), [NOTCH2 p.Arg2104Gly](/variant/notch2-p-arg2104gly).

### 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 4861130). 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.*