CLIP1 p.Val385=
c.1155G>C · VCV4229917
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, eas)
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 0.6 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 13.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,902 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00916%
Overall
0.00291%
47/1,614,126 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,490 |
| Admixed American | 0.015% | 6,668 |
| Finnishnot grpmax-eligible | 0.0109% | 9,148 |
| South Asian | 0.00659% | 15,182 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| African / African-American | 0.004% | 24,985 |
| European (non-Finnish) | 0.000763% | 131,116 |
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.Val385=
- Coding
- c.1155G>C
- MANE Select
- NM_001247997
- Type
- single nucleotide variant
- Location
- chr12:122355163 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 11 PDB
- Residue 385
- an α-helix
Similar variants
- CLIP1 p.Val385Met Uncertain significance ★ ⚠ same residue
- 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.Asn99= Benign/Likely 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-val385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown