CLASP2 p.Thr1127=
c.3381A>G · rs377121956 · VCV3040123
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.372%, sas)
Conditions
1
CLASP2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.037 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.58 | GERP -0.27, phastCons 0.057 |
| Overall | ||
| CADD | 7.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.372%
South Asian · 338/90,890 alleles
Filtering AF
0.339%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.326%
Overall
0.0254%
407/1,604,240 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.372% | 269 |
| Middle Eastern | 0.0826% | 1,210 |
| Remaining individualsnot grpmax-eligible | 0.029% | 3,452 |
| European (non-Finnish) | 0.00384% | 26,023 |
| African / African-American | 0.00134% | 74,810 |
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.Thr1127=
- Coding
- c.3381A>G
- MANE Select
- NM_001365631
- dbSNP
- rs377121956
- Type
- single nucleotide variant
- Location
- chr3:33543456 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98 · 7 PDB
- Residue 1127
- an α-helix; the 'interaction with rsn and localization to the golgi and kinetochores' region; the 'required for cortical localization' region
Disease context
CLASP2-related disorder
Similar variants
- CLASP2 c.2240-4C>G Uncertain significance same condition
- CLASP2 c.1694+8C>T Likely benign same condition
- CLASP2 c.2455-1147C>G Benign same condition
- CLASP2 p.Ala1461= Benign same condition
- CLASP2 p.Asn872= Likely benign same condition
- CLASP2 p.Asp1262= Likely benign same condition
- CLASP2 p.Asp1442= Likely benign same condition
- CLASP2 p.Glu2= Likely benign same condition
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-thr1127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown