Is FBXO7 p.Phe424= (c.1272C>T) pathogenic?

FBXO7 p.Phe424= (c.1272C>T) is classified Benign in FBXO7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-19). Rare (popmax 0.426%, amr); Associated with parkinsonian-pyramidal syndrome.

What condition is associated with FBXO7 p.Phe424= (c.1272C>T)?

FBXO7 p.Phe424= (c.1272C>T) is associated with parkinsonian-pyramidal syndrome (ClinVar).

How common is FBXO7 p.Phe424= (c.1272C>T) in the general population?

FBXO7 p.Phe424= (c.1272C>T) is rare (popmax 0.426%, amr) (gnomAD).

How is Parkinsonian-pyramidal syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FBXO7 p.Phe424=

c.1272C>T · rs577160947 · VCV770014

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.426%, amr)

Conditions

parkinsonian-pyramidal syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.055	GERP -2.5, phastCons 0.86
Overall
CADD	5.641	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.426% Admixed American · 256/60,028 alleles

Filtering AF 0.384% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.367%

Overall 0.0212% 343/1,614,236 alleles · rare exomes 326/1,461,888 · genomes 17/152,348 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.426%	234
European (non-Finnish)	0.00678%	14,751
Remaining individualsnot grpmax-eligible	0.0064%	15,627
African / African-American	0.00266%	37,528
East Asian	0.00223%	44,890

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: FBXO7
Protein: p.Phe424=
Coding: c.1272C>T
MANE Select: NM_012179
dbSNP: rs577160947
Type: single nucleotide variant
Location: chr22:32498233 (GRCh38)
Gene constraint: LOEUF 0.955 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 67.13 · 2 PDB
Residue 424: the 'important for interaction with cdk6' region

Full FBXO7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

parkinsonian-pyramidal syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Parkinsonian-pyramidal syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult

Similar variants

FBXO7 p.Phe424Tyr Benign ★ same residue
FBXO7 p.Arg321Ter Pathogenic/Likely pathogenic ★★ same condition
FBXO7 p.Arg345Ter Pathogenic/Likely pathogenic ★★ same condition
FBXO7 p.Arg381Ter Pathogenic/Likely pathogenic ★★ same condition
FBXO7 p.Arg45Ter Pathogenic/Likely pathogenic ★★ same condition
FBXO7 p.Arg498Ter Pathogenic ★★ same condition
FBXO7 p.Gln237Ter Pathogenic/Likely pathogenic ★★ same condition
FBXO7 p.Thr22Met Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/fbxo7-p-phe424 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown