# NM_000789.4(ACE):c.899del (p.Phe300fs)

https://sugi.bio/variant/ace-p-phe300fs

## Summary

**ACE p.Phe300fs (c.899del)** is classified **Pathogenic** in ACE (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-01). Very rare (popmax 0.00167%, amr); Associated with renal tubular dysgenesis.

**At a glance:** Pathogenic · review: Single submitter · rsID rs1387186484 · 1 submitter · 1 linked condition · very rare (popmax 0.00167%, amr)

## For patients & families {#patients}

This is a change in the ACE gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to renal tubular dysgenesis.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0000379/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ACE](https://sugi.bio/atlas/gene/ACE/) |
| Protein change (HGVS p.) | p.Phe300fs |
| Coding change (HGVS c.) | c.899del |
| MANE Select transcript | [NM_000789](https://www.ncbi.nlm.nih.gov/nuccore/NM_000789) |
| dbSNP | [rs1387186484](https://www.ncbi.nlm.nih.gov/snp/rs1387186484/) |
| Variant type | Deletion |
| Location | chr17:63481140-63481140 (GRCh38) |
| ClinVar | [VCV974413](https://www.ncbi.nlm.nih.gov/clinvar/variation/974413/) |

**All HGVS expressions:** `NC_000017.10:g.61558503del`, `NC_000017.11:g.63481142del`, `NG_011648.1:g.9070del`, `NM_000789.4:c.899del`, `NM_001382700.1:c.426del`, `NM_001382701.1:c.47del`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **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 7.632, GERP 1.84, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.88, pLI 6.2381e-32. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 6 of 25**, 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 **0.00167%** (amr) · 1/59,990 in the highest group · 3/1,613,856 alleles overall — very rare (popmax 0.00167%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00167% | 59,990 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,498 |
| European (non-Finnish) | 8.47e-05% | 1,179,988 |

*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}

**ACE** population constraint: LOEUF 0.88, pLI 6.2381e-32, missense-Z -0.50314. *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):

- **renal tubular dysgenesis - ACE** — Definitive (AR)

## Protein context {#protein}

Residue **300** lies in the peptidase m2 1 domain.

AlphaFold model confidence (whole protein): pLDDT 91.38, 82% of residues very-high.

**97 experimental structure(s)** (PDB): [1O86](https://www.rcsb.org/structure/1O86), [1O8A](https://www.rcsb.org/structure/1O8A), [1UZE](https://www.rcsb.org/structure/1UZE), [1UZF](https://www.rcsb.org/structure/1UZF), [2C6F](https://www.rcsb.org/structure/2C6F), [2C6N](https://www.rcsb.org/structure/2C6N) — incl. mutant structure 2IUL.

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

*Describes the biological roles of ACE (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:** ACE's established molecular role includes actin binding. p.Phe300fs falls in the peptidase m2 1 domain.


### Pathways affected {#pathways}

ACE participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Metabolism of Angiotensinogen to Angiotensins](https://reactome.org/content/detail/R-HSA-2022377) | curated |

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

**Molecular function:** actin binding, endopeptidase activity, metalloendopeptidase activity, peptidase activity, metallopeptidase activity, exopeptidase activity.

**Biological process:** kidney development, angiotensin maturation, regulation of systemic arterial blood pressure by renin-angiotensin, substance P catabolic process, bradykinin catabolic process, hormone metabolic process.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2020-02-01.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Molecular Biology Laboratory, Fundació Puigvert | Pathogenic | criteria provided, single submitter | research | 2020-02-01 |

## Associated conditions {#conditions}

[renal tubular dysgenesis](https://sugi.bio/atlas/disease/renal-tubular-dysgenesis/).

**Reported phenotype names (ClinVar):** Renal tubular dysgenesis, Renotubular dysgenesis.

## Similar variants {#similar}

Related ACE variant pages (same residue, condition, or type): [ACE p.Ser5fs](/variant/ace-p-ser5fs), [ACE p.Leu454fs](/variant/ace-p-leu454fs), [ACE p.Leu16_Pro23del](/variant/ace-p-leu16-pro23del), [ACE p.Leu440fs](/variant/ace-p-leu440fs), [ACE c.1709+5G>C](/variant/ace-c-1709-plus-5g-c), [ACE c.3503+1G>C](/variant/ace-c-3503-plus-1g-c), [ACE p.Arg496Ter](/variant/ace-p-arg496ter), [ACE p.Arg508Ter](/variant/ace-p-arg508ter).

### 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 974413). 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.*