Is CUL9 p.Arg102= (c.306A>G) pathogenic?

CUL9 p.Arg102= (c.306A>G) is classified Uncertain significance in CUL9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-15). Absent from gnomAD v4.1; Associated with CUL9-related disorder.

What condition is associated with CUL9 p.Arg102= (c.306A>G)?

CUL9 p.Arg102= (c.306A>G) is associated with CUL9-related disorder (ClinVar).

How common is CUL9 p.Arg102= (c.306A>G) in the general population?

CUL9 p.Arg102= (c.306A>G) is absent from gnomAD v4.1 (gnomAD).

CUL9 p.Arg102=

c.306A>G · VCV3353798

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CUL9-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.57 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.4	GERP -2.3, phastCons 0.3
Overall
CADD	13.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CUL9
Protein: p.Arg102=
Coding: c.306A>G
MANE Select: NM_015089
Type: single nucleotide variant
Location: chr6:43184616 (GRCh38)
Gene constraint: LOEUF 0.334 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.64 · 4 PDB

Full CUL9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CUL9-related disorder

Similar variants

CUL9 p.Arg102Gln Uncertain significance ★ ⚠ same residue
CUL9 p.Cys2171Trp Uncertain significance ★ same condition
CUL9 p.Thr2301Ile Uncertain significance ★ ⚠ same condition
CUL9 p.Ala2306Val Uncertain significance ⚠ same condition
CUL9 c.2389-7C>A Likely benign same condition
CUL9 c.3051-8C>T Benign same condition
CUL9 c.3384+9C>T Likely benign same condition
CUL9 c.5023-7C>T Likely benign 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/cul9-p-arg102 (accessed [today's date]).

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