CLUAP1 p.Asp379=
c.1137C>T · rs377189683 · VCV1108383
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0717%, amr)
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 -3.1 | GERP -3.6 |
| Overall | ||
| CADD | 0.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0717%
Admixed American · 43/60,008 alleles
Filtering AF
0.0546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0486%
Overall
0.00446%
72/1,614,016 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0717% | 1,396 |
| Middle Eastern | 0.0495% | 2,021 |
| African / African-American | 0.0107% | 9,377 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| East Asian | 0.00223% | 44,860 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000932% | 107,272 |
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
- CLUAP1
- Protein
- p.Asp379=
- Coding
- c.1137C>T
- MANE Select
- NM_015041
- dbSNP
- rs377189683
- Type
- single nucleotide variant
- Location
- chr16:3536166 (GRCh38)
- Gene constraint
- LOEUF 1.23 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.02
- Residue 379
- the 'disordered' region
Similar variants
- CLUAP1 p.Asp379Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CLUAP1 p.Ala152Glu Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Ala188Gly Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Ala339Thr Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg20Gln Uncertain significance ★★ same type
- CLUAP1 p.Arg228Gln Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg304His Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg332Gln 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/cluap1-p-asp379 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown