CLASP2 p.Leu28Phe
c.82C>T · rs550533307 · VCV2269163
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.051%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.212 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP -2, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 73 kb · p 0.71 · regional, not allelic |
| Overall | ||
| CADD | 19.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.051%
East Asian · 21/41,170 alleles
Filtering AF
0.0341%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0286%
Overall
0.00284%
44/1,551,532 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.051% | 1,960 |
| African / African-American | 0.0259% | 3,858 |
| Remaining individualsnot grpmax-eligible | 0.00332% | 30,087 |
| Admixed American | 0.00195% | 51,186 |
| European (non-Finnish) | 8.71e-05% | 1,148,372 |
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
- CLASP2
- Protein
- p.Leu28Phe
- Coding
- c.82C>T
- MANE Select
- NM_001365631
- dbSNP
- rs550533307
- Type
- single nucleotide variant
- Location
- chr3:33717921 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98 · 7 PDB
- Residue 28
- the 'disordered' region
Similar variants
- CLASP2 c.1949-9C>T Benign ★★ same type
- CLASP2 p.Gly57= Benign ★★ same type
- CLASP2 p.Ser544= Benign ★★ same type
- CLASP2 c.2068+1G>A Uncertain significance ★ same type
- CLASP2 c.2455-1137A>C Uncertain significance ★ same type
- CLASP2 p.Ala1209Gly Uncertain significance ★ ⚠ same type
- CLASP2 p.Ala1251Pro Uncertain significance ★ ⚠ same type
- CLASP2 p.Ala1402Val 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/clasp2-p-leu28phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown