CD164 p.Thr113=
c.339G>A · rs373906087 · VCV1326617
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0785%, afr)
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 0.54 | GERP -3.7 |
| Overall | ||
| CADD | 3.897 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0785%
African / African-American · 56/71,318 alleles
Filtering AF
0.062%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0562%
Overall
0.00557%
87/1,561,358 alleles · ultra-rare
exomes 40/1,409,322 · genomes 47/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0785% | 1,274 |
| Admixed American | 0.0115% | 8,696 |
| Remaining individualsnot grpmax-eligible | 0.00998% | 10,016 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00364% | 27,470 |
| European (non-Finnish) | 0.00163% | 61,327 |
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.Thr113=
- Coding
- c.339G>A
- MANE Select
- NM_006016
- dbSNP
- rs373906087
- Type
- single nucleotide variant
- Location
- chr6:109376105 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
Similar variants
- CD164 p.Thr113Met 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-thr113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown