CLIP1 p.Gln457=
c.1371A>G · rs117592229 · VCV2643498
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 0.74, phastCons 1 |
| Overall | ||
| CADD | 19.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
European (non-Finnish) · 12,297/1,130,782 alleles
Filtering AF
1.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.913%
13,665/1,496,404 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.09% | 92 |
| Remaining individualsnot grpmax-eligible | 0.673% | 149 |
| Finnishnot grpmax-eligible | 0.668% | 150 |
| Admixed American | 0.532% | 188 |
| Middle Eastern | 0.42% | 238 |
| South Asian | 0.369% | 271 |
| Ashkenazi Jewishnot grpmax-eligible | 0.234% | 426 |
| African / African-American | 0.14% | 712 |
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.Gln457=
- Coding
- c.1371A>G
- MANE Select
- NM_001247997
- dbSNP
- rs117592229
- Type
- single nucleotide variant
- Location
- chr12:122351141 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 11 PDB
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.Asn99= Benign/Likely benign ★★ same type
- CLIP1 p.Lys851= 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-gln457 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown