CLUAP1 p.Lys125=
c.375G>A · rs1278135388 · VCV1987878
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00205%, 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 -0.034 | GERP -4, phastCons 0.047 |
| Overall | ||
| CADD | 1.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00205%
Admixed American · 1/48,790 alleles
Overall
0.00014%
2/1,426,402 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00205% | 48,790 |
| European (non-Finnish) | 8.54e-05% | 1,170,437 |
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.Lys125=
- Coding
- c.375G>A
- MANE Select
- NM_015041
- dbSNP
- rs1278135388
- Type
- single nucleotide variant
- Location
- chr16:3508444 (GRCh38)
- Gene constraint
- LOEUF 1.23 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.02
Similar variants
- 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
- CLUAP1 p.Asn296Lys 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-lys125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown