CUL4B p.Ala90=
c.270T>C · rs371312556 · VCV1609573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00527%, afr)
Conditions
1
X-linked intellectual disability, Cabezas type
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 4.4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00527%
African / African-American · 3/56,955 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000688%
Overall
0.000249%
3/1,205,796 alleles · very rare
exomes 2/1,094,088 · genomes 1/111,708 · joint denominator
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
- CUL4B
- Protein
- p.Ala90=
- Coding
- c.270T>C
- MANE Select
- NM_001079872
- dbSNP
- rs371312556
- Type
- single nucleotide variant
- Location
- chrX:120560369 (GRCh38)
- Structure
- AlphaFold pLDDT 80.02 · 5 PDB
- Residue 90
- the 'disordered' region
Similar variants
- CUL4B p.Arg351Ter Likely pathogenic ★★ same condition
- CUL4B p.Arg370Ter Pathogenic ★★ same condition
- CUL4B p.Gln241Ter Pathogenic ★★ same condition
- CUL4B p.Thr813= Pathogenic/Likely pathogenic ★★ same condition
- CUL4B c.2592+3A>T Uncertain significance ★★ same condition
- CUL4B c.777-3C>T Uncertain significance ★★ same condition
- CUL4B p.Ala16Pro Uncertain significance ★★ ⚠ same condition
- CUL4B p.Cys712Arg 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-ala90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown