CCR9 p.Leu136=
c.406C>T · rs35423527 · VCV780381
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.07%, 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 0.77 | GERP -4.2, phastCons 0.5 |
| Overall | ||
| CADD | 7.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.07%
African / African-American · 2,305/75,022 alleles
Filtering AF
2.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.93%
Overall
0.161%
2,598/1,614,166 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.07% | 33 |
| Admixed American | 0.22% | 455 |
| Remaining individualsnot grpmax-eligible | 0.195% | 512 |
| Middle Eastern | 0.0495% | 2,020 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00254% | 39,334 |
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
- CCR9
- Protein
- p.Leu136=
- Coding
- c.406C>T
- MANE Select
- NM_001296 · reported on NM_031200
- dbSNP
- rs35423527
- Type
- single nucleotide variant
- Location
- chr3:45901194 (GRCh38)
- Structure
- AlphaFold pLDDT 80.89 · 3 PDB
- Residue 136
- a disulfide bond
Similar variants
- CCR10 p.Leu267Met Uncertain significance ★★ ⚠ same type
- CCR10 p.Pro155= Benign ★★ same type
- ACKR2 p.Ala248Thr Uncertain significance ★ ⚠ same type
- ACKR2 p.Cys284Arg Uncertain significance ★ same type
- ACKR2 p.His317Tyr Uncertain significance ★ ⚠ same type
- ACKR2 p.Ile56Val Uncertain significance ★ ⚠ same type
- ACKR2 p.Leu59Trp Uncertain significance ★ ⚠ same type
- ACKR2 p.Ser172Cys 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/ccr9-p-leu136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown