# NM_001114753.3(ENG):c.392del (p.Pro131fs)

https://sugi.bio/variant/eng-p-pro131fs

## Summary

**ENG p.Pro131fs (c.392del)** is classified **Pathogenic** in ENG (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-05). Very rare (popmax 8.47e-05%, nfe); Associated with Cardiovascular phenotype.

**At a glance:** Pathogenic · review: Multiple submitters · rsID rs1554810510 · 4 submitters · 3 linked conditions · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the ENG gene that is considered disease-causing, submitted by 4 submitters, 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 | [ENG](https://sugi.bio/atlas/gene/ENG/) |
| Protein change (HGVS p.) | p.Pro131fs |
| Coding change (HGVS c.) | c.392del |
| MANE Select transcript | [NM_001114753](https://www.ncbi.nlm.nih.gov/nuccore/NM_001114753) |
| dbSNP | [rs1554810510](https://www.ncbi.nlm.nih.gov/snp/rs1554810510/) |
| Variant type | Deletion |
| Location | chr9:127826641-127826641 (GRCh38) |
| ClinVar | [VCV458347](https://www.ncbi.nlm.nih.gov/clinvar/variation/458347/) |

**All HGVS expressions:** `LRG_589:g.33128del`, `LRG_589t1:c.392del`, `LRG_589t2:c.392del`, `NC_000009.11:g.130588924del`, `NC_000009.12:g.127826645del`, `NG_009551.1:g.33128del`, `NM_000118.3:c.392delC`, `NM_000118.4:c.388delC`, `NM_001114753.1:c.392delC`, `NM_001114753.2:c.388delC`, `NM_001114753.3:c.392del`, `NM_001278138.2:c.-155del`, `NM_001406715.1:c.388delC`

## 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 -2.909, GERP -4.1 — fast-evolving / accelerated position
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. ClinGen curates **sufficient evidence for haploinsufficiency** in this gene (constraint LOEUF 0.374, pLI 1), supporting a loss-of-function disease mechanism. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 4 of 15**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **8.47e-05%** (nfe) · 1/1,179,996 in the highest group · 1/1,461,746 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}

**ENG** population constraint: LOEUF 0.374, pLI 1, missense-Z 1.285; ClinGen dosage — haploinsufficiency 3, 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):

- **juvenile polyposis syndrome** — Limited (AD)
- **telangiectasia, hereditary hemorrhagic, type 1** — Definitive (AD)

## Protein context {#protein}

Residue **131** lies in a disulfide bond; the 'required for interaction with gdf2' region; the 'or2' region.

AlphaFold model confidence (whole protein): pLDDT 80.84, 40% of residues very-high.

**3 experimental structure(s)** (PDB): [5HZV](https://www.rcsb.org/structure/5HZV), [5HZW](https://www.rcsb.org/structure/5HZW), [5I04](https://www.rcsb.org/structure/5I04).

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

*Describes the biological roles of ENG (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:** ENG's established molecular role includes type II transforming growth factor beta receptor binding. p.Pro131fs falls in the required for interaction with gdf2 region.


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

**Molecular function:** type II transforming growth factor beta receptor binding, galactose binding, glycosaminoglycan binding, coreceptor activity, signaling receptor activator activity, type I transforming growth factor beta receptor binding.

**Biological process:** negative regulation of transcription by RNA polymerase II, vasculogenesis, response to hypoxia, negative regulation of endothelial cell proliferation, positive regulation of systemic arterial blood pressure, regulation of DNA-templated transcription.

## Clinical significance {#significance}

**Pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-08-05.

**Submitter consensus:** unanimous (4/4 Pathogenic).

**Submission history:** 4 submissions (2019–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| New York Genome Center | Pathogenic | criteria provided, single submitter | clinical testing | 2019-09-13 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2025-08-05 |
| Genomics And Bioinformatics Analysis Resource, Columbia University | Pathogenic | no assertion criteria provided | research |  |
| Ambry Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2024-07-26 |

## Associated conditions {#conditions}

[Cardiovascular phenotype](https://sugi.bio/atlas/disease/cardiovascular-phenotype/), [telangiectasia, hereditary hemorrhagic, type 1](https://sugi.bio/atlas/disease/telangiectasia-hereditary-hemorrhagic-type-1/), [hereditary hemorrhagic telangiectasia](https://sugi.bio/atlas/disease/hereditary-hemorrhagic-telangiectasia/).

**Reported phenotype names (ClinVar):** Cardiovascular phenotype, Hereditary hemorrhagic telangiectasia, Telangiectasia, hereditary hemorrhagic, type 1, Osler Weber Rendu syndrome type 1, ENG-Related Hereditary Hemorrhagic Telangiectasia, ORW DISEASE, Osler Weber Rendu syndrome, OSLER-RENDU-WEBER DISEASE, Osler hemorrhagic telangiectasia syndrome.

## Similar variants {#similar}

Related ENG variant pages (same residue, condition, or type): [ENG p.Pro131Leu](/variant/eng-p-pro131leu), [ENG p.Pro131Ala](/variant/eng-p-pro131ala), [ENG p.Pro131=](/variant/eng-p-pro131), [ENG p.Pro131Gln](/variant/eng-p-pro131gln), [ENG p.Val568fs](/variant/eng-p-val568fs), [ENG c.1687delG](/variant/eng-c-1687delg), [ENG p.Ala312fs](/variant/eng-p-ala312fs), [ENG p.Ala55fs](/variant/eng-p-ala55fs).

### 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 458347). 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.*