CILP p.Ser189=
c.567C>T · rs146295641 · VCV2645457
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.481%, 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 -7.6 | GERP -3.1 |
| Overall | ||
| CADD | 0.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.481%
African / African-American · 361/75,016 alleles
Filtering AF
0.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.424%
Overall
0.0254%
410/1,613,986 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.481% | 208 |
| Middle Eastern | 0.0828% | 1,208 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,464 |
| Admixed American | 0.0183% | 5,456 |
| South Asian | 0.00549% | 18,215 |
| European (non-Finnish) | 0.00119% | 84,286 |
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
- CILP
- Protein
- p.Ser189=
- Coding
- c.567C>T
- MANE Select
- NM_003613
- dbSNP
- rs146295641
- Type
- single nucleotide variant
- Location
- chr15:65205324 (GRCh38)
- Gene constraint
- LOEUF 1.077 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.30
- Residue 189
- a disulfide bond; the tsp type-1 domain
Similar variants
- CILP p.Leu1064= Benign ★★ same type
- CILP p.Ala1003Asp Uncertain significance ★ ⚠ same type
- CILP p.Ala102Val Uncertain significance ★ ⚠ same type
- CILP p.Ala1053Thr Uncertain significance ★ ⚠ same type
- CILP p.Ala1091Thr Uncertain significance ★ ⚠ same type
- CILP p.Ala1091Val Uncertain significance ★ ⚠ same type
- CILP p.Ala1114Gly Uncertain significance ★ ⚠ same type
- CILP p.Ala1143Thr Uncertain significance ★ ⚠ 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/cilp-p-ser189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown