CLUH p.Thr401=
c.1203G>A · VCV3494052
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.183%, eas)
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 -11 | GERP -4.7 |
| Overall | ||
| CADD | 2.819 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.183%
East Asian · 82/44,870 alleles
Filtering AF
0.151%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.139%
Overall
0.00701%
113/1,613,066 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.183% | 547 |
| Admixed American | 0.0233% | 4,285 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| South Asian | 0.0033% | 30,304 |
| African / African-American | 0.00266% | 37,524 |
| European (non-Finnish) | 0.000339% | 294,938 |
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
- CLUH
- Protein
- p.Thr401=
- Coding
- c.1203G>A
- MANE Select
- NM_001366661
- Type
- single nucleotide variant
- Location
- chr17:2700445 (GRCh38)
- Gene constraint
- LOEUF 0.799 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.11
- Residue 401
- the clu domain
Similar variants
- CLUH p.Thr401Met Uncertain significance ★ ⚠ same residue
- CLUH p.Ala671Val Benign ★★ same type
- CLUH p.Ala700= Likely benign ★★ same type
- CLUH p.Glu1228= Likely benign ★★ same type
- CLUH p.Thr201= Benign ★★ same type
- CLUH c.1025+1G>A Uncertain significance ★ same type
- CLUH p.Ala1076Thr Uncertain significance ★ ⚠ same type
- CLUH p.Ala1257Ser Uncertain significance ★ ⚠ 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/cluh-p-thr401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown