CLASP2 p.Pro170=
c.510A>G · rs143967899 · VCV3037912
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.54%, amr)
Conditions
1
CLASP2-related disorder
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 -0.23 | GERP 0.23, phastCons 0.6 |
| Overall | ||
| CADD | 10.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.54%
Admixed American · 2,675/58,916 alleles
Filtering AF
4.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.34%
Overall
2.1%
33,708/1,602,464 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.54% | 22 |
| Finnishnot grpmax-eligible | 3.73% | 27 |
| European (non-Finnish) | 2.25% | 44 |
| Remaining individualsnot grpmax-eligible | 2.03% | 49 |
| Ashkenazi Jewishnot grpmax-eligible | 0.751% | 133 |
| African / African-American | 0.44% | 227 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| South Asian | 0.426% | 235 |
| Middle Eastern | 0.253% | 395 |
| East Asian | 0.0875% | 1,142 |
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.Pro170=
- Coding
- c.510A>G
- MANE Select
- NM_001365631
- dbSNP
- rs143967899
- Type
- single nucleotide variant
- Location
- chr3:33687096 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98 · 7 PDB
- Residue 170
- the 'tog 1' region; an α-helix
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-pro170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown