Is CUL9 p.Asp2080= (c.6240C>T) pathogenic?

CUL9 p.Asp2080= (c.6240C>T) is classified Likely benign in CUL9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-24). Rare (popmax 0.367%, sas); Associated with CUL9-related disorder.

What condition is associated with CUL9 p.Asp2080= (c.6240C>T)?

CUL9 p.Asp2080= (c.6240C>T) is associated with CUL9-related disorder (ClinVar).

How common is CUL9 p.Asp2080= (c.6240C>T) in the general population?

CUL9 p.Asp2080= (c.6240C>T) is rare (popmax 0.367%, sas) (gnomAD).

CUL9 p.Asp2080=

c.6240C>T · rs778436960 · VCV3043966

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.367%, sas)

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 -12	GERP -3.9
Overall
CADD	0.091	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.367% South Asian · 333/90,830 alleles

Filtering AF 0.334% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.321%

Overall 0.0354% 568/1,604,396 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.367%	273
Middle Eastern	0.0332%	3,014
Remaining individualsnot grpmax-eligible	0.0226%	4,427
European (non-Finnish)	0.0177%	5,663
Admixed American	0.01%	9,971
African / African-American	0.00535%	18,697
Finnishnot grpmax-eligible	0.00314%	31,896

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: CUL9
Protein: p.Asp2080=
Coding: c.6240C>T
MANE Select: NM_015089
dbSNP: rs778436960
Type: single nucleotide variant
Location: chr6:43216461 (GRCh38)
Gene constraint: LOEUF 0.334 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.64 · 4 PDB
Residue 2080: the 'triad supradomain' region

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-asp2080 (accessed [today's date]).

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