Is FBXO7 p.Asp92His (c.274G>C) pathogenic?

FBXO7 p.Asp92His (c.274G>C) is classified Uncertain significance in FBXO7 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-12-19). AlphaMissense: likely benign (0.2278); Ultra-rare (popmax 0.0791%, sas); Associated with parkinsonian-pyramidal syndrome.

What condition is associated with FBXO7 p.Asp92His (c.274G>C)?

FBXO7 p.Asp92His (c.274G>C) is associated with parkinsonian-pyramidal syndrome (ClinVar).

How common is FBXO7 p.Asp92His (c.274G>C) in the general population?

FBXO7 p.Asp92His (c.274G>C) is ultra-rare (popmax 0.0791%, sas) (gnomAD).

How is Parkinsonian-pyramidal syndrome inherited?

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

What do computational predictors say about FBXO7 p.Asp92His (c.274G>C)?

AlphaMissense predicts likely benign (score 0.2278) — an in-silico prediction, not a clinical call.

FBXO7 p.Asp92His

c.274G>C · rs139135860 · VCV341308

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.2278 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0791%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

parkinsonian-pyramidal syndrome

Computational evidence

Protein change
AlphaMissense	0.2278	likely benign
REVEL	0.158	moderately benign-leaning
SaProt	LLR -6.52	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.37	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 24 kb · p 0.42 · regional, not allelic
Overall
CADD	26.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0791% South Asian · 72/91,080 alleles

Filtering AF 0.0643% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0589%

Overall 0.0151% 244/1,614,020 alleles · ultra-rare exomes 220/1,461,892 · genomes 24/152,128 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0791%	1,265
Finnishnot grpmax-eligible	0.039%	2,561
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0128%	7,811
European (non-Finnish)	0.0114%	8,806
African / African-American	0.00401%	24,965
Admixed American	0.00167%	59,994

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.Asp92His
Coding: c.274G>C
MANE Select: NM_012179
dbSNP: rs139135860
Type: single nucleotide variant
Location: chr22:32479132 (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 92: the 'disordered' region; the 'important for interaction with pink1' 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

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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
FBXO7 p.Ala84Val Uncertain significance ★★ ⚠ 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-asp92his (accessed [today's date]).

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