# NM_004444.5(EPHB4):c.2458C>T (p.Pro820Ser)

https://sugi.bio/variant/ephb4-p-pro820ser

## Summary

**EPHB4 p.Pro820Ser (c.2458C>T)** is classified **Uncertain significance** in EPHB4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-22). AlphaMissense: likely pathogenic (0.9993); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1584653653 · 1 submitter · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the EPHB4 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 | [EPHB4](https://sugi.bio/atlas/gene/EPHB4/) |
| Protein change (HGVS p.) | p.Pro820Ser |
| Coding change (HGVS c.) | c.2458C>T |
| MANE Select transcript | [NM_004444](https://www.ncbi.nlm.nih.gov/nuccore/NM_004444) |
| dbSNP | [rs1584653653](https://www.ncbi.nlm.nih.gov/snp/rs1584653653/) |
| Variant type | single nucleotide variant |
| Location | chr7:100806446-100806446 (GRCh38) |
| ClinVar | [VCV2693799](https://www.ncbi.nlm.nih.gov/clinvar/variation/2693799/) |

**All HGVS expressions:** `NC_000007.13:g.100404068G>A`, `NC_000007.14:g.100806446G>A`, `NG_052671.1:g.26076C>T`, `NG_084625.2:g.1104G>A`, `NM_004444.5:c.2458C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9993)
- REVEL 0.827 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -12.218 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 11.919, GERP 2.49, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 2%** most-pathogenic-predicted substitutions in EPHB4 (of 5,740 modeled).
- CADD: **PHRED 33.0**. 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 0.87** across the covering region of the MANE Select transcript (100,803,464–100,806,466), spanning 3,002 bp. Chi-square p 0.042. 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 (G>C, Δ0.28 donor 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: **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}

**EPHB4** population constraint: LOEUF 0.645, pLI 4.3123e-06, missense-Z 1.6946. *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):

- **EPHB4-associated vascular malformation spectrum** — Definitive (AD)

## Protein context {#protein}

Residue **820** lies in a turn; a UniProt-annotated variant site (in cmavm2); a UniProt-annotated variant site (in cmavm2; uncertain significance); the protein kinase domain.

AlphaFold model confidence (whole protein): pLDDT 82.46, 48% of residues very-high.

**23 experimental structure(s)** (PDB): [2BBA](https://www.rcsb.org/structure/2BBA), [2E7H](https://www.rcsb.org/structure/2E7H), [2HLE](https://www.rcsb.org/structure/2HLE), [2QKQ](https://www.rcsb.org/structure/2QKQ), [2VWU](https://www.rcsb.org/structure/2VWU), [2VWV](https://www.rcsb.org/structure/2VWV).

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

*Describes the biological roles of EPHB4 (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:** EPHB4's established molecular role includes ephrin receptor activity. p.Pro820Ser falls in the protein kinase domain.


### Pathways affected {#pathways}

EPHB4 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [EPH-ephrin mediated repulsion of cells](https://reactome.org/content/detail/R-HSA-3928665) | curated |
| [EPH-Ephrin signaling](https://reactome.org/content/detail/R-HSA-2682334) | electronic |
| [EPHB-mediated forward signaling](https://reactome.org/content/detail/R-HSA-3928662) | electronic |
| [Ephrin signaling](https://reactome.org/content/detail/R-HSA-3928664) | electronic |

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

**Molecular function:** ephrin receptor activity.

**Biological process:** angiogenesis, cell migration involved in sprouting angiogenesis, cell adhesion, ephrin receptor signaling pathway.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-08-22.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-08-22 |

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

## Similar variants {#similar}

Related EPHB4 variant pages (same residue, condition, or type): [EPHB4 p.Pro820Gln](/variant/ephb4-p-pro820gln), [EPHB4 p.Pro820Leu](/variant/ephb4-p-pro820leu), [EPHB4 p.Pro820Thr](/variant/ephb4-p-pro820thr), [EPHB4 p.Pro820=](/variant/ephb4-p-pro820), [EPHB4 c.1691+1G>A](/variant/ephb4-c-1691-plus-1g-a), [EPHB4 c.2484+1G>A](/variant/ephb4-c-2484-plus-1g-a), [EPHB4 p.Arg269Ter](/variant/ephb4-p-arg269ter), [EPHB4 p.Arg365Ter](/variant/ephb4-p-arg365ter).

### 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 2026-07-14); 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 2693799). 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.*