CD320 p.Ser210=
c.630T>A · rs1599620901 · VCV682210
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00203%, nfe)
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 -0.43 | GERP -0.16, phastCons 0.001 |
| Overall | ||
| CADD | 1.771 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00203%
European (non-Finnish) · 24/1,179,998 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.00164%
24/1,461,880 alleles · very rare
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
- CD320
- Protein
- p.Ser210=
- Coding
- c.630T>A
- MANE Select
- NM_016579
- dbSNP
- rs1599620901
- Type
- single nucleotide variant
- Location
- chr19:8302853 (GRCh38)
- Gene constraint
- LOEUF 1.488 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.61 · 6 PDB
- Residue 210
- the 'disordered' region
Similar variants
- CD320 p.Arg129Leu Uncertain significance ★★ ⚠ same type
- CD320 p.Arg138Ser Uncertain significance ★★ same type
- CD320 p.Arg254Gln Uncertain significance ★★ ⚠ same type
- CD320 p.Arg258His Uncertain significance ★★ ⚠ same type
- CD320 p.Asn170Ser Uncertain significance ★★ ⚠ same type
- CD320 p.Asp143Asn Uncertain significance ★★ ⚠ same type
- CD320 p.Asp160Asn Uncertain significance ★★ same type
- CD320 p.Gly166Val 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/cd320-p-ser210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown