CCL20 p.Cys74=
c.222C>T · rs150823624 · VCV733334
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.03%, sas)
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 -0.83 | GERP -4, phastCons 0.016 |
| Overall | ||
| CADD | 5.468 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.03%
South Asian · 1,846/90,878 alleles
Filtering AF
1.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.92%
Overall
0.127%
2,048/1,611,014 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.03% | 49 |
| Remaining individualsnot grpmax-eligible | 0.143% | 701 |
| East Asian | 0.112% | 896 |
| Middle Eastern | 0.0331% | 3,023 |
| African / African-American | 0.00801% | 12,491 |
| European (non-Finnish) | 0.0045% | 22,218 |
| Admixed American | 0.00334% | 29,957 |
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
- CCL20
- Protein
- p.Cys74=
- Coding
- c.222C>T
- MANE Select
- NM_004591
- dbSNP
- rs150823624
- Type
- single nucleotide variant
- Location
- chr2:227816337 (GRCh38)
- Gene constraint
- LOEUF 1.849 · pLI 0.33 (gnomAD)
- Structure
- AlphaFold pLDDT 89.36 · 6 PDB
- Residue 74
- a β-strand; a disulfide bond
Similar variants
- CCL20 p.Arg87Cys Uncertain significance ★ ⚠ same type
- CCL20 p.Asn61Ser Uncertain significance ★ ⚠ same type
- CCL20 p.Gly57Val Uncertain significance ★ ⚠ same type
- CCL20 p.Ile64Val Uncertain significance ★ ⚠ same type
- CCL20 p.Leu9Pro Uncertain significance ★ ⚠ same type
- CCL20 p.Ser14Leu Uncertain significance ★ ⚠ same type
- CCL20 p.Arg39His Likely benign ★ ⚠ same type
- CCL20 p.Arg51Gln 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/ccl20-p-cys74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown