CD4 p.Phe123=
c.369C>T · rs11064416 · VCV714504
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.29%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.35 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.047 | GERP -2.2, phastCons 0.001 |
| Overall | ||
| CADD | 13.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.29%
African / African-American · 2,467/74,946 alleles
Filtering AF
3.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.14%
Overall
0.18%
2,907/1,613,462 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.29% | 30 |
| Admixed American | 0.298% | 335 |
| Remaining individualsnot grpmax-eligible | 0.219% | 456 |
| Middle Eastern | 0.132% | 756 |
| European (non-Finnish) | 0.00949% | 10,533 |
| South Asian | 0.0033% | 30,336 |
| East Asian | 0.00223% | 44,870 |
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.Phe123=
- Coding
- c.369C>T
- MANE Select
- NM_000616
- dbSNP
- rs11064416
- Type
- single nucleotide variant
- Location
- chr12:6814296 (GRCh38)
- Gene constraint
- LOEUF 0.673 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.35 · 84 PDB
- Residue 123
- the ig-like v-type domain; a β-strand
Similar variants
- CD4 p.Phe123Leu Uncertain significance ★ ⚠ same residue
- 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
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-phe123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown