CC2D1B p.Leu511=
c.1533G>T · rs62000427 · VCV771309
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.77%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.008 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -1.1, phastCons 0.25 |
| Overall | ||
| CADD | 6.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.77%
Admixed American · 1,584/57,104 alleles
Filtering AF
2.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.61%
Overall
0.744%
11,856/1,593,640 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.77% | 36 |
| South Asian | 1.09% | 92 |
| European (non-Finnish) | 0.728% | 137 |
| Remaining individualsnot grpmax-eligible | 0.598% | 167 |
| Finnishnot grpmax-eligible | 0.488% | 205 |
| Middle Eastern | 0.22% | 456 |
| African / African-American | 0.128% | 784 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0395% | 2,531 |
| East Asian | 0.00893% | 11,193 |
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
- CC2D1B
- Protein
- p.Leu511=
- Coding
- c.1533G>T
- MANE Select
- NM_001330585
- dbSNP
- rs62000427
- Type
- single nucleotide variant
- Location
- chr1:52357827 (GRCh38)
- Gene constraint
- LOEUF 0.978 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
- Residue 511
- the 'disordered' region
Similar variants
- CC2D1B p.Gly790= Benign ★★ same type
- CC2D1B p.His674Tyr Likely benign ★★ same type
- CC2D1B p.Ala103Gly Uncertain significance ★ ⚠ same type
- CC2D1B p.Ala180Ser Uncertain significance ★ ⚠ same type
- CC2D1B p.Ala181Thr Uncertain significance ★ ⚠ same type
- CC2D1B p.Ala181Val Uncertain significance ★ ⚠ same type
- CC2D1B p.Ala208Thr Uncertain significance ★ ⚠ same type
- CC2D1B p.Ala251Thr 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/cc2d1b-p-leu511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown