CD164 p.Leu183=
c.549T>G · rs375553590 · VCV1659053
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00305%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.7 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 5.534 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00305%
European (non-Finnish) · 36/1,179,744 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00229%
37/1,613,322 alleles · very rare
exomes 35/1,461,106 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00305% | 32,771 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,444 |
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
- CD164
- Protein
- p.Leu183=
- Coding
- c.549T>G
- MANE Select
- NM_006016
- dbSNP
- rs375553590
- Type
- single nucleotide variant
- Location
- chr6:109368896 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
Similar variants
- CD164 p.Leu183Pro Uncertain significance ★★ ⚠ same residue
- CD164 p.Arg192Ter Uncertain significance ★★ same type
- CD164 p.Asn121Ser Uncertain significance ★★ ⚠ same type
- CD164 p.Asn32Lys Uncertain significance ★★ ⚠ same type
- CD164 p.Asp107Asn Uncertain significance ★★ ⚠ same type
- CD164 p.Leu15Val Uncertain significance ★★ ⚠ same type
- CD164 p.Leu9Phe Uncertain significance ★★ ⚠ same type
- CD164 p.Lys137Gln 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/cd164-p-leu183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown