CLIP2 p.Pro116=
c.348G>A · VCV4821575
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00932%, 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 -14 | GERP -15 |
| Overall | ||
| CADD | 1.226 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00932%
East Asian · 4/42,940 alleles
Filtering AF
0.00317%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00186%
Overall
0.0021%
30/1,427,418 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00932% | 10,735 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00344% | 29,040 |
| European (non-Finnish) | 0.00206% | 48,591 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,340 |
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.Pro116=
- Coding
- c.348G>A
- MANE Select
- NM_003388
- Type
- single nucleotide variant
- Location
- chr7:74338674 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 2 PDB
- Residue 116
- the cap-gly 1 domain; a β-strand
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.Leu169= 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-pro116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown