CD6 p.Pro454=
c.1362G>A · rs376880399 · VCV3042003
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, nfe)
Conditions
1
CD6-related disorder
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 -1.7 | GERP -3.1 |
| Overall | ||
| CADD | 6.465 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
European (non-Finnish) · 499/1,179,664 alleles
Filtering AF
0.0392%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.038%
Overall
0.0327%
527/1,613,198 alleles · ultra-rare
exomes 499/1,461,086 · genomes 28/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0423% | 2,364 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,163 |
| Middle Eastern | 0.0164% | 6,082 |
| African / African-American | 0.00935% | 10,698 |
| Admixed American | 0.00334% | 29,932 |
| Finnishnot grpmax-eligible | 0.00312% | 32,015 |
| East Asian | 0.00223% | 44,802 |
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
- CD6
- Protein
- p.Pro454=
- Coding
- c.1362G>A
- MANE Select
- NM_006725
- dbSNP
- rs376880399
- Type
- single nucleotide variant
- Location
- chr11:61013989 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.14 · 1 PDB
Disease context
CD6-related disorder
Similar variants
- CD6 c.49+8C>T Benign same condition
- CD6 p.Ala257= Benign same condition
- CD6 p.Ala257Val Benign same condition
- CD6 p.Ala271Thr Benign same condition
- CD6 p.Ala605= Benign same condition
- CD6 p.Arg225Trp Benign same condition
- CD6 p.Gly606Ser Benign same condition
- CD6 p.Pro433= Likely benign same condition
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/cd6-p-pro454 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown