CLASP2 p.Ser795=
c.2385G>A · VCV4003255
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0825%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -5 |
| Overall | ||
| CADD | 3.602 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0825%
East Asian · 37/44,870 alleles
Filtering AF
0.0615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.00459%
74/1,613,714 alleles · ultra-rare
exomes 64/1,461,514 · genomes 10/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0825% | 1,213 |
| South Asian | 0.0264% | 3,794 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,234 |
| European (non-Finnish) | 0.000932% | 107,251 |
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.Ser795=
- Coding
- c.2385G>A
- MANE Select
- NM_001365631
- Type
- single nucleotide variant
- Location
- chr3:33576238 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98 · 7 PDB
- Residue 795
- the 'tog 2' region
Similar variants
- CLASP2 p.Ser795Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser795 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown