CD300A p.Thr23=
c.69C>T · VCV3488022
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.129%, 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 -20 | GERP -4 |
| Overall | ||
| CADD | 0.412 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.129%
East Asian · 58/44,878 alleles
Filtering AF
0.103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.093%
Overall
0.00582%
94/1,613,852 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.129% | 774 |
| South Asian | 0.0198% | 5,059 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,928 |
| African / African-American | 0.00799% | 12,509 |
| Admixed American | 0.00167% | 60,008 |
| European (non-Finnish) | 0.000339% | 294,959 |
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
- CD300A
- Protein
- p.Thr23=
- Coding
- c.69C>T
- MANE Select
- NM_007261
- Type
- single nucleotide variant
- Location
- chr17:74473564 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.59 · 1 PDB
- Residue 23
- a β-strand; the ig-like v-type domain
Similar variants
- CD300A p.Ala6Thr Uncertain significance ★ ⚠ same type
- CD300A p.Ala98Gly Uncertain significance ★ ⚠ same type
- CD300A p.Arg262Gly Uncertain significance ★ ⚠ same type
- CD300A p.Arg285Pro Uncertain significance ★ ⚠ same type
- CD300A p.Asn176Tyr Uncertain significance ★ ⚠ same type
- CD300A p.Cys103Tyr Uncertain significance ★ ⚠ same type
- CD300A p.Cys15Tyr Uncertain significance ★ ⚠ same type
- CD300A p.Glu173Asp 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/cd300a-p-thr23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown