CLCC1 p.Thr201=
c.603T>C · rs338466 · VCV1166559
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 72.8%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -6.2 | GERP -3.1 |
| Overall | ||
| CADD | 1.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
72.8%
African / African-American · 54,582/74,932 alleles
Filtering AF
72.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 72.1%
Overall
53.3%
860,027/1,613,108 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 72.8% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 57.5% | 2 |
| Middle Eastern | 57% | 2 |
| Admixed American | 56% | 2 |
| Remaining individualsnot grpmax-eligible | 53.2% | 2 |
| European (non-Finnish) | 53% | 2 |
| Finnishnot grpmax-eligible | 48.2% | 2 |
| South Asian | 46.4% | 2 |
| East Asian | 43.4% | 2 |
| Amishnot grpmax-eligible | 36.5% | 3 |
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
- CLCC1
- Protein
- p.Thr201=
- Coding
- c.603T>C
- MANE Select
- NM_001377458
- dbSNP
- rs338466
- Type
- single nucleotide variant
- Location
- chr1:108943574 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.13
Similar variants
- CLCC1 p.Thr201Ala Uncertain significance ★ ⚠ same residue
- CLCC1 p.Asp25Glu Pathogenic/Likely pathogenic ★★ same type
- CLCC1 p.Ala245Thr Uncertain significance ★★ ⚠ same type
- CLCC1 p.Ala522Thr Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg208His Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg377Trp Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg381Trp Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg401Gly 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/clcc1-p-thr201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown