CLASP1 p.Lys534=
c.1602A>G · rs374803325 · VCV2651323
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, 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 -0.45 | GERP -1, phastCons 0.099 |
| Overall | ||
| CADD | 5.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,942 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00721%
Overall
0.00136%
22/1,613,866 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,245 |
| South Asian | 0.00768% | 13,013 |
| Admixed American | 0.00167% | 60,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
| European (non-Finnish) | 8.48e-05% | 1,179,870 |
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
- CLASP1
- Protein
- p.Lys534=
- Coding
- c.1602A>G
- MANE Select
- NM_001395891
- dbSNP
- rs374803325
- Type
- single nucleotide variant
- Location
- chr2:121449042 (GRCh38)
- Gene constraint
- LOEUF 0.237 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.44 · 3 PDB
- Residue 534
- an α-helix
Similar variants
- CLASP1 c.196-567G>A Pathogenic/Likely pathogenic ★★ same type
- CLASP1 c.196-570C>T Pathogenic/Likely pathogenic ★★ same type
- CLASP1 c.196-594G>A Pathogenic/Likely pathogenic ★★ same type
- CLASP1 c.196-605C>T Pathogenic/Likely pathogenic ★★ same type
- CLASP1 c.196-670T>G Pathogenic/Likely pathogenic ★★ same type
- CLASP1 n.30G>A Likely pathogenic ★★ same type
- MAST1 p.Gly517Ser Pathogenic ★★ same type
- MAST1 p.Pro1177Leu Likely pathogenic ★★ ⚠ 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/clasp1-p-lys534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown