CCR1 p.Arg338=
c.1014G>A · rs150288365 · VCV708388
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.666%, 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 -0.005 | GERP -0.51, phastCons 0.001 |
| Overall | ||
| CADD | 9.243 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.666%
African / African-American · 500/75,034 alleles
Filtering AF
0.618%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.599%
Overall
0.0356%
574/1,614,124 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.666% | 150 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,084 |
| Admixed American | 0.0317% | 3,159 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,543 |
| European (non-Finnish) | 0.00186% | 53,636 |
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.Arg338=
- Coding
- c.1014G>A
- MANE Select
- NM_001295
- dbSNP
- rs150288365
- Type
- single nucleotide variant
- Location
- chr3:46203300 (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-arg338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown