# NM_012179.4(FBXO7):c.1536_1539del (p.Arg513fs)

https://sugi.bio/variant/fbxo7-p-arg513fs

## Summary

**FBXO7 p.Arg513fs (c.1536_1539del)** is classified **Uncertain significance** in FBXO7 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-06-20). Ultra-rare (popmax 0.0365%, nfe); Associated with parkinsonian-pyramidal syndrome.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs772175765 · 5 submitters · 1 linked condition · ultra-rare (popmax 0.0365%, nfe)

## For patients & families {#patients}

This is a change in the FBXO7 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 5 submitters, and is linked to parkinsonian-pyramidal syndrome.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Adolescent, Adult |
| Diagnostic panels | FBXO7 is a diagnostic-grade gene on 7 Genomics England panels |

**Commonly reported features of Parkinsonian-pyramidal syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Parkinsonism — Obligate (100%)
- Abnormal pyramidal sign — Obligate (100%)
- Neurogenic bladder — Frequent (79-30%)
- Hypomimic face — Frequent (79-30%)
- Slow saccadic eye movements — Frequent (79-30%)
- Spasticity — Frequent (79-30%)
- Dystonia — Frequent (79-30%)
- Myoclonus — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0009175/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [FBXO7](https://sugi.bio/atlas/gene/FBXO7/) |
| Protein change (HGVS p.) | p.Arg513fs |
| Coding change (HGVS c.) | c.1536_1539del |
| MANE Select transcript | [NM_012179](https://www.ncbi.nlm.nih.gov/nuccore/NM_012179) |
| dbSNP | [rs772175765](https://www.ncbi.nlm.nih.gov/snp/rs772175765/) |
| Variant type | Deletion |
| Location | chr22:32498495-32498498 (GRCh38) |
| ClinVar | [VCV640811](https://www.ncbi.nlm.nih.gov/clinvar/variation/640811/) |

**All HGVS expressions:** `NC_000022.10:g.32894484_32894487del`, `NC_000022.11:g.32498497_32498500del`, `NG_016001.2:g.28778_28781del`, `NM_001033024.2:c.1299_1302del`, `NM_001257990.2:c.1194_1197del`, `NM_012179.3:c.1536_1539delTCGG`, `NM_012179.4:c.1536_1539del`, `NM_012179.4:c.1536_1539delTCGG`

## 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 1.964, GERP 0.614, phastCons 1 — weakly conserved position
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.955, pLI 2.9822e-07. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in the last exon (9 of 9)** — predicted to **escape NMD**, so the truncated protein is likely expressed. An input to PVS1, not an applied code.
- CADD: **PHRED 34.0**. 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.*
- 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 **0.0365%** (nfe) · FAF95 0.0337% · FAF99 0.0325% · 431/1,180,032 in the highest group · 460/1,613,904 alleles overall — ultra-rare (popmax 0.0365%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0416% | 2,403 |
| European (non-Finnish) (grpmax) | 0.0365% | 2,738 |
| African / African-American | 0.00401% | 24,964 |

Remaining individuals shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**FBXO7** population constraint: LOEUF 0.955, pLI 2.9822e-07, missense-Z -0.0088092; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity Not yet evaluated/3. *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 **513** lies in the 'important for interaction with cdk6' region; the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 67.13, 13% of residues very-high.

**2 experimental structure(s)** (PDB): [4L9C](https://www.rcsb.org/structure/4L9C), [4L9H](https://www.rcsb.org/structure/4L9H).

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

*Describes the biological roles of FBXO7 (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:** FBXO7's established molecular role includes protein kinase binding. p.Arg513fs falls in the important for interaction with cdk6 region.


### Pathways affected {#pathways}

FBXO7 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Antigen processing: Ubiquitination & Proteasome degradation](https://reactome.org/content/detail/R-HSA-983168) | curated |
| [Neddylation](https://reactome.org/content/detail/R-HSA-8951664) | curated |

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

**Molecular function:** protein kinase binding, ubiquitin protein ligase binding, ubiquitin binding, protein heterodimerization activity, ubiquitin-like ligase-substrate adaptor activity.

**Biological process:** autophagy of mitochondrion, ubiquitin-dependent protein catabolic process, obsolete protein targeting to mitochondrion, regulation of neuron projection development, protein ubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-06-20.

**Submitter consensus:** unanimous (5/5 Uncertain significance).

**Submission history:** 5 submissions (2022–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Fulgent Genetics, Fulgent Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-02-15 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-08-09 |
| Department of Pathology and Laboratory Medicine, Sinai Health System | Uncertain significance | criteria provided, single submitter | research | 2022-11-25 |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-10-25 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2026-06-20 |

## Associated conditions {#conditions}

[parkinsonian-pyramidal syndrome](https://sugi.bio/atlas/disease/parkinsonian-pyramidal-syndrome/).

**Reported phenotype names (ClinVar):** Parkinsonian-pyramidal syndrome, not provided, not specified, PALLIDOPYRAMIDAL SYNDROME, PARKINSON DISEASE 15, AUTOSOMAL RECESSIVE EARLY-ONSET, PARKINSON DISEASE 15, AUTOSOMAL RECESSIVE, AllHighlyPenetrant, none provided.

## Similar variants {#similar}

Related FBXO7 variant pages (same residue, condition, or type): [FBXO7 p.Arg513Trp](/variant/fbxo7-p-arg513trp), [FBXO7 p.Pro484fs](/variant/fbxo7-p-pro484fs), [FBXO7 c.1183-2_1183-1del](/variant/fbxo7-c-1183-minus-2-1183-minus-1del), [FBXO7 p.Asn51fs](/variant/fbxo7-p-asn51fs), [FBXO7 p.Asp348fs](/variant/fbxo7-p-asp348fs), [FBXO7 p.Cys192fs](/variant/fbxo7-p-cys192fs), [FBXO7 p.Gly126fs](/variant/fbxo7-p-gly126fs), [FBXO7 p.Leu106fs](/variant/fbxo7-p-leu106fs).

### 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 640811). 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.*