CLIP2 p.Leu169=
c.505C>T · rs142629570 · VCV773890
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.308%, amr)
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 1.4 | GERP 5.2, phastCons 1 |
| Overall | ||
| CADD | 9.153 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.308%
Admixed American · 185/59,996 alleles
Filtering AF
0.272%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.258%
Overall
0.0163%
263/1,611,028 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.308% | 324 |
| African / African-American | 0.0614% | 1,629 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,940 |
| East Asian | 0.00223% | 44,886 |
| European (non-Finnish) | 0.00186% | 53,633 |
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
- CLIP2
- Protein
- p.Leu169=
- Coding
- c.505C>T
- MANE Select
- NM_003388
- dbSNP
- rs142629570
- Type
- single nucleotide variant
- Location
- chr7:74338831 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 2 PDB
Similar variants
- CLIP2 p.Arg12His Uncertain significance ★★ ⚠ same type
- CLIP2 p.Ala123= Benign ★★ same type
- CLIP2 p.Arg932= Benign ★★ same type
- CLIP2 p.Asn205= Benign ★★ same type
- CLIP2 p.Asn910= Benign/Likely benign ★★ same type
- CLIP2 p.His159= Benign/Likely benign ★★ same type
- CLIP2 p.Ile396= Benign ★★ same type
- CLIP2 p.Pro179Ser 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/clip2-p-leu169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown