CCR1 p.Ser332=
c.996C>T · rs202159281 · VCV726052
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00934%, 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 -0.092 | GERP -4.4 |
| Overall | ||
| CADD | 8.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00934%
African / African-American · 7/74,922 alleles
Filtering AF
0.00511%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00508%
82/1,614,052 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00934% | 10,703 |
| European (non-Finnish) | 0.00627% | 15,946 |
| East Asian | 0.00223% | 44,886 |
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
- CCR1
- Protein
- p.Ser332=
- Coding
- c.996C>T
- MANE Select
- NM_001295
- dbSNP
- rs202159281
- Type
- single nucleotide variant
- Location
- chr3:46203318 (GRCh38)
- Gene constraint
- LOEUF 1.931 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 83.49 · 3 PDB
Similar variants
- CCR1 p.Ala159Val Likely benign ★★ same type
- CCR1 p.Leu127= Benign ★★ same type
- CCR1 p.Leu54= Benign/Likely benign ★★ same type
- CCR1 p.Ter356= Benign ★★ same type
- CCR1 p.Thr146= Likely benign ★★ same type
- CCR1 p.Tyr291His Benign ★★ same type
- CCR1 p.Tyr301= Benign/Likely benign ★★ same type
- CCR1 p.Ala159Ser 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/ccr1-p-ser332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown