CDR2 p.Leu6=
c.18G>A · rs151255507 · VCV2646314
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -0.48 | phastCons 0.003 |
| Overall | ||
| CADD | 7.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,038 alleles
Filtering AF
0.00642%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00595%
Overall
0.00625%
100/1,601,188 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,038 |
| European (non-Finnish) | 0.00775% | 12,907 |
| Remaining individualsnot grpmax-eligible | 0.00646% | 15,469 |
| East Asian | 0.00231% | 43,356 |
| South Asian | 0.00223% | 44,749 |
| African / African-American | 0.00137% | 73,084 |
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
- CDR2
- Protein
- p.Leu6=
- Coding
- c.18G>A
- MANE Select
- NM_001802
- dbSNP
- rs151255507
- Type
- single nucleotide variant
- Location
- chr16:22374292 (GRCh38)
- Gene constraint
- LOEUF 0.879 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.84
Similar variants
- CDR2 p.Ala107Val Uncertain significance ★ ⚠ same type
- CDR2 p.Ala155Thr Uncertain significance ★ ⚠ same type
- CDR2 p.Ala178Thr Uncertain significance ★ ⚠ same type
- CDR2 p.Ala252Pro Uncertain significance ★ ⚠ same type
- CDR2 p.Ala319Ser Uncertain significance ★ ⚠ same type
- CDR2 p.Ala355Thr Uncertain significance ★ ⚠ same type
- CDR2 p.Ala394Thr Uncertain significance ★ ⚠ same type
- CDR2 p.Arg213Gln 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/cdr2-p-leu6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown