CD4 p.Thr233=
c.699G>A · rs10849525 · VCV743449
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00466%, 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 -0.42 | GERP -1.3 |
| Overall | ||
| CADD | 5.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00466%
European (non-Finnish) · 55/1,180,036 alleles
Filtering AF
0.00367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00329%
Overall
0.00384%
62/1,614,162 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00466% | 21,455 |
| East Asian | 0.00445% | 22,447 |
| African / African-American | 0.00267% | 37,505 |
| Admixed American | 0.00167% | 60,014 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
| South Asian | 0.0011% | 91,080 |
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
- CD4
- Protein
- p.Thr233=
- Coding
- c.699G>A
- MANE Select
- NM_000616
- dbSNP
- rs10849525
- Type
- single nucleotide variant
- Location
- chr12:6816147 (GRCh38)
- Gene constraint
- LOEUF 0.673 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.35 · 84 PDB
- Residue 233
- the ig-like c2-type 2 domain
Similar variants
- CD4 p.Ser352Trp Uncertain significance ★★ ⚠ same type
- CD4 p.Thr444Ala Uncertain significance ★★ ⚠ same type
- CD4 c.1346+55T>G Benign ★★ same type
- CD4 c.49+35A>G Benign ★★ same type
- CD4 c.*91C>A Benign ★★ same type
- CD4 c.*92A>G Benign ★★ same type
- CD4 p.Arg265Trp Benign ★★ ⚠ same type
- CD4 p.Arg431Gln Benign/Likely benign ★★ ⚠ 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/cd4-p-thr233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown