CLU p.Val406=
c.1218C>T · rs755605617 · VCV3043325
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
Conditions
1
CLU-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.029 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -2.6 |
| Overall | ||
| CADD | 2.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,912 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00223%
36/1,614,022 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,485 |
| South Asian | 0.00329% | 30,363 |
| European (non-Finnish) | 0.00229% | 43,705 |
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
- CLU
- Protein
- p.Val406=
- Coding
- c.1218C>T
- MANE Select
- NM_001831
- dbSNP
- rs755605617
- Type
- single nucleotide variant
- Location
- chr8:27598582 (GRCh38)
- Gene constraint
- LOEUF 0.716 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.11 · 2 PDB
- Residue 406
- a β-strand
Disease context
CLU-related disorder
Similar variants
- CLU c.*9T>C Likely benign same condition
- CLU p.Arg182His Likely benign same condition
- CLU p.Lys40= Likely benign same condition
- CLU p.Val20= Likely benign same condition
- CLU p.Ala438= Likely benign ★★ same type
- CLU p.Asn64= Likely benign ★★ same type
- CLU p.Asp328= Benign ★★ same type
- CLU p.Asp328Asn Benign ★★ same type
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/clu-p-val406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown