Is CUL9 p.Tyr152= (c.456C>T) pathogenic?

CUL9 p.Tyr152= (c.456C>T) is classified Benign in CUL9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-02). Low-frequency (popmax 1.39%, afr); Associated with CUL9-related disorder.

What condition is associated with CUL9 p.Tyr152= (c.456C>T)?

CUL9 p.Tyr152= (c.456C>T) is associated with CUL9-related disorder (ClinVar).

How common is CUL9 p.Tyr152= (c.456C>T) in the general population?

CUL9 p.Tyr152= (c.456C>T) is low-frequency (popmax 1.39%, afr) (gnomAD).

CUL9 p.Tyr152=

c.456C>T · rs115556089 · VCV3042127

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.39%, afr)

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 -8.4	GERP -3.8
Overall
CADD	0.839	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.39% African / African-American · 1,047/75,058 alleles

Filtering AF 1.32% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.3%

Overall 0.0867% 1,399/1,614,172 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.39%	72
Admixed American	0.163%	613
Remaining individualsnot grpmax-eligible	0.152%	658
Middle Eastern	0.148%	674
European (non-Finnish)	0.0118%	8,490
South Asian	0.011%	9,109
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608

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.Tyr152=
Coding: c.456C>T
MANE Select: NM_015089
dbSNP: rs115556089
Type: single nucleotide variant
Location: chr6:43184766 (GRCh38)
Gene constraint: LOEUF 0.334 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.64 · 4 PDB
Residue 152: an α-helix

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-tyr152 (accessed [today's date]).

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