CLIP1 p.Ser1189=
c.3567C>T · rs375267504 · VCV2643497
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0103%, nfe)
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 1.2 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 7.734 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0103%
European (non-Finnish) · 122/1,180,034 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00828%
Overall
0.00812%
131/1,612,956 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0103% | 9,672 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,799 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Admixed American | 0.00333% | 29,996 |
| Finnishnot grpmax-eligible | 0.00312% | 32,012 |
| African / African-American | 0.00134% | 74,896 |
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.Ser1189=
- Coding
- c.3567C>T
- MANE Select
- NM_001247997
- dbSNP
- rs375267504
- Type
- single nucleotide variant
- Location
- chr12:122309789 (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-ser1189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown