CD164 c.331+255del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 48.3%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +255 | deep intronic (+255 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3.5 |
| Non-coding constraint | Z -1.98 | 1 kb window · o/e 1.15 · regional · uncalibrated |
| Overall | ||
| CADD | 0.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
48.3%
South Asian · 2,188/4,532 alleles
Filtering AF
46.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 45.9%
Overall
28.3%
40,002/141,324 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 48.3% | 2 |
| East Asian | 39.2% | 3 |
| Amishnot grpmax-eligible | 36.5% | 3 |
| Admixed American | 35% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 31.8% | 3 |
| Finnishnot grpmax-eligible | 31.4% | 3 |
| Remaining individualsnot grpmax-eligible | 30.6% | 3 |
| Middle Eastern | 30.6% | 3 |
| European (non-Finnish) | 29.8% | 3 |
| African / African-American | 18.1% | 6 |
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
- Coding
- c.331+255del
- MANE Select
- NM_006016
- dbSNP
- rs35168490
- Type
- Deletion
- Location
- chr6:109377645 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
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-c-331-plus-255del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown