CLASP2 p.Ser544=
c.1632T>C · rs61734242 · VCV785037
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.9%, 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 1.5 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 9.996 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.9%
African / African-American · 2,177/75,022 alleles
Filtering AF
2.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.76%
Overall
0.186%
3,001/1,613,750 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.9% | 34 |
| Middle Eastern | 0.676% | 148 |
| Admixed American | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.272% | 367 |
| European (non-Finnish) | 0.0372% | 2,687 |
| South Asian | 0.00659% | 15,180 |
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.Ser544=
- Coding
- c.1632T>C
- MANE Select
- NM_001365631
- dbSNP
- rs61734242
- Type
- single nucleotide variant
- Location
- chr3:33606653 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98 · 7 PDB
- Residue 544
- the 'interaction with microtubules, mapre1 and mapre3' region; the 'disordered' region
Similar variants
- CLASP2 c.1949-9C>T Benign ★★ same type
- CLASP2 p.Gly57= 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
- CLASP2 p.Ala1496Pro 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-ser544 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown