CLUAP1 p.Ser314=
c.942G>A · rs751331352 · VCV1536415
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 -9.3 | GERP -5.1 |
| Overall | ||
| CADD | 0.208 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,868 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.0018%
29/1,613,568 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,717 |
| European (non-Finnish) | 0.00203% | 49,159 |
| Admixed American | 0.00167% | 59,978 |
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.Ser314=
- Coding
- c.942G>A
- MANE Select
- NM_015041
- dbSNP
- rs751331352
- Type
- single nucleotide variant
- Location
- chr16:3530581 (GRCh38)
- Gene constraint
- LOEUF 1.23 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.02
- Residue 314
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- CLUAP1 p.Ser314Leu Uncertain significance ★ ⚠ 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-ser314 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown