CD164 p.Ser5=
c.15C>T · rs373195063 · VCV2980526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00484%, eas)
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 -0.27 | GERP -3.3 |
| Overall | ||
| CADD | 3.419 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00484%
East Asian · 2/41,300 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000485%
Overall
0.00103%
16/1,547,650 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00484% | 20,650 |
| Admixed American | 0.00193% | 51,904 |
| European (non-Finnish) | 0.00113% | 88,670 |
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.Ser5=
- Coding
- c.15C>T
- MANE Select
- NM_006016
- dbSNP
- rs373195063
- Type
- single nucleotide variant
- Location
- chr6:109382364 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
Similar variants
- CD164 p.Ser5Tyr 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.Leu183Pro Uncertain significance ★★ ⚠ same type
- CD164 p.Leu9Phe 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-ser5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown