CLIP2 p.His159=
c.477C>T · rs111609508 · VCV790596
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.33%, 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 0.36 | GERP 3.1, phastCons 0.99 |
| Overall | ||
| CADD | 3.695 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.33%
African / African-American · 995/75,046 alleles
Filtering AF
1.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.23%
Overall
0.162%
2,615/1,611,308 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.33% | 75 |
| Middle Eastern | 1.04% | 96 |
| Admixed American | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.357% | 280 |
| European (non-Finnish) | 0.0903% | 1,108 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,972 |
| South Asian | 0.0242% | 4,138 |
| East Asian | 0.00223% | 44,862 |
| Finnishnot grpmax-eligible | 0.00163% | 61,506 |
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.His159=
- Coding
- c.477C>T
- MANE Select
- NM_003388
- dbSNP
- rs111609508
- Type
- single nucleotide variant
- Location
- chr7:74338803 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 2 PDB
- Residue 159
- the 'disordered' region
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.Ile396= Benign ★★ same type
- CLIP2 p.Leu169= 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-his159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown