Is CUL9 p.Pro1147= (c.3441C>G) pathogenic?

CUL9 p.Pro1147= (c.3441C>G) is classified Likely benign in CUL9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-13). Absent from gnomAD v4.1; Associated with CUL9-related disorder.

What condition is associated with CUL9 p.Pro1147= (c.3441C>G)?

CUL9 p.Pro1147= (c.3441C>G) is associated with CUL9-related disorder (ClinVar).

How common is CUL9 p.Pro1147= (c.3441C>G) in the general population?

CUL9 p.Pro1147= (c.3441C>G) is absent from gnomAD v4.1 (gnomAD).

CUL9 p.Pro1147=

c.3441C>G · rs2533677165 · VCV3041064

Likely benign No assertion criteria

Classification

Likely benign

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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.84	GERP -1.4, phastCons 0.003
Overall
CADD	8.049	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.Pro1147=
Coding: c.3441C>G
MANE Select: NM_015089
dbSNP: rs2533677165
Type: single nucleotide variant
Location: chr6:43200492 (GRCh38)
Gene constraint: LOEUF 0.334 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.64 · 4 PDB
Residue 1147: the doc domain

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

Disease context

CUL9-related disorder

Similar variants

CUL9 p.Cys2171Trp Uncertain significance ★ same condition
CUL9 p.Thr2301Ile Uncertain significance ★ ⚠ same condition
CUL9 p.Ala2306Val Uncertain significance ⚠ same condition
CUL9 p.Arg102= 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-pro1147 (accessed [today's date]).

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