CLIP1 p.Asn99=
c.297C>T · rs141383610 · VCV434787
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.422%, 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 -3.8 | GERP -3.8 |
| Overall | ||
| CADD | 0.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.422%
African / African-American · 316/74,932 alleles
Filtering AF
0.383%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.368%
Overall
0.0234%
377/1,613,850 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.422% | 237 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| Admixed American | 0.0367% | 2,725 |
| South Asian | 0.011% | 9,107 |
| East Asian | 0.00223% | 44,848 |
| European (non-Finnish) | 0.000254% | 393,329 |
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
- CLIP1
- Protein
- p.Asn99=
- Coding
- c.297C>T
- MANE Select
- NM_001247997
- dbSNP
- rs141383610
- Type
- single nucleotide variant
- Location
- chr12:122377749 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 11 PDB
- Residue 99
- the cap-gly 1 domain; the 'important for tubulin binding' region; a β-strand
Similar variants
- CLIP1 p.Ala142Val Uncertain significance ★★ ⚠ same type
- CLIP1 p.Arg342Cys Uncertain significance ★★ ⚠ same type
- CLIP1 p.Gly1356Arg Uncertain significance ★★ ⚠ same type
- CLIP1 p.Lys1267Arg Uncertain significance ★★ ⚠ same type
- CLIP1 p.Ala1224Ser Likely benign ★★ same type
- CLIP1 p.Ala301= Benign ★★ same type
- CLIP1 p.Lys851= Likely benign ★★ same type
- CLIP1 p.Ser102= Benign ★★ 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/clip1-p-asn99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown