CUL4B p.Asp346=
c.1038T>C · rs759619904 · VCV1789764
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00257%, nfe)
Conditions
1
Inborn genetic diseases
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 2.3 | GERP -5.5, phastCons 1 |
| Overall | ||
| CADD | 7.224 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00257%
European (non-Finnish) · 23/894,773 alleles
Filtering AF
0.00171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00143%
Overall
0.0019%
23/1,209,696 alleles · very rare
exomes 22/1,097,586 · genomes 1/112,110 · 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.Asp346=
- Coding
- c.1038T>C
- MANE Select
- NM_001079872
- dbSNP
- rs759619904
- Type
- single nucleotide variant
- Location
- chrX:120544526 (GRCh38)
- Structure
- AlphaFold pLDDT 80.02 · 5 PDB
- Residue 346
- an α-helix
Similar variants
- CUL4B p.His397Tyr Uncertain significance ★★ ⚠ same condition
- CUL4B p.Ser166Pro Uncertain significance ★★ ⚠ same condition
- CUL4B c.1324+15G>A Benign ★★ same condition
- CUL4B p.Arg878= Benign/Likely benign ★★ same condition
- CUL4B p.Asp884= Likely benign ★★ same condition
- CUL4B p.Cys619= Benign/Likely benign ★★ same condition
- CUL4B p.Gln388= Benign/Likely benign ★★ same condition
- CUL4B p.Gly9Glu Benign/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/cul4b-p-asp346 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown