Is CUL4B p.Ser5= (c.15A>C) pathogenic?

CUL4B p.Ser5= (c.15A>C) is classified Likely benign in CUL4B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-05-12). Absent from gnomAD v4.1; Associated with CUL4B-related disorder.

What condition is associated with CUL4B p.Ser5= (c.15A>C)?

CUL4B p.Ser5= (c.15A>C) is associated with CUL4B-related disorder (ClinVar).

How common is CUL4B p.Ser5= (c.15A>C) in the general population?

CUL4B p.Ser5= (c.15A>C) is absent from gnomAD v4.1 (gnomAD).

CUL4B p.Ser5=

c.15A>C · VCV3353778

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

CUL4B-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 0.18	GERP -0.17, phastCons 0.12
Overall
CADD	3.174	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: CUL4B
Protein: p.Ser5=
Coding: c.15A>C
MANE Select: NM_001079872 · reported on NM_003588
Type: single nucleotide variant
Location: chrX:120574603 (GRCh38)
Structure: AlphaFold pLDDT 80.02 · 5 PDB
Residue 5: the 'disordered' region

Full CUL4B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CUL4B-related disorder

Similar variants

CUL4B p.Ser5Ala Uncertain significance ★ ⚠ same residue
CUL4B p.Gly5= Likely benign ★ same residue
CUL4B c.1852+1G>T Pathogenic ★ same condition
CUL4B c.2267-2A>G Likely pathogenic ★ same condition
CUL4B p.Ile318Ser Uncertain significance ★ ⚠ same condition
CUL4B p.Ser456Phe Uncertain significance ★ ⚠ same condition
CUL4B p.Glu221Asp Uncertain significance ⚠ same condition
CUL4B p.Lys782Arg 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/cul4b-p-ser5 (accessed [today's date]).

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