CD163 p.Leu867=
c.2599C>T · rs61729513 · VCV776691
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.28%, 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 2.1 | GERP 0.13, phastCons 0.99 |
| Overall | ||
| CADD | 9.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.28%
African / African-American · 3,215/75,050 alleles
Filtering AF
4.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.11%
Overall
0.239%
3,861/1,614,198 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.28% | 23 |
| Admixed American | 0.398% | 251 |
| Remaining individualsnot grpmax-eligible | 0.336% | 298 |
| Middle Eastern | 0.149% | 673 |
| South Asian | 0.0154% | 6,506 |
| European (non-Finnish) | 0.0147% | 6,782 |
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
- CD163
- Protein
- p.Leu867=
- Coding
- c.2599C>T
- MANE Select
- NM_203416
- dbSNP
- rs61729513
- Type
- single nucleotide variant
- Location
- chr12:7485276 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.72 · 14 PDB
- Residue 867
- the srcr 8 domain; an α-helix; a disulfide bond
Similar variants
- CD163 c.3344-24C>A Benign ★★ same type
- CD163 c.3344-56G>A Likely benign ★★ same type
- CD163 c.457+9T>A Benign ★★ same type
- CD163 p.Asn642Lys Benign ★★ same type
- CD163 p.Asn892= Benign ★★ same type
- CD163 p.Cys1008= Benign ★★ same type
- CD163 p.Ile342Val Benign ★★ ⚠ same type
- CD163 p.Ser570Asn 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/cd163-p-leu867 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown