CC2D1B p.Ser133=
c.399T>G · rs41311156 · VCV2638814
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.352%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.02 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.83 | GERP -2.1, phastCons 0.48 |
| Overall | ||
| CADD | 4.057 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.352%
European (non-Finnish) · 4,148/1,180,012 alleles
Filtering AF
0.343%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.339%
Overall
0.283%
4,565/1,614,124 alleles · rare
exomes 4,312/1,461,886 · genomes 253/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.352% | 284 |
| Remaining individualsnot grpmax-eligible | 0.254% | 393 |
| South Asian | 0.154% | 651 |
| Admixed American | 0.0616% | 1,622 |
| Finnishnot grpmax-eligible | 0.0531% | 1,883 |
| African / African-American | 0.0453% | 2,206 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,467 |
| East Asian | 0.00223% | 44,874 |
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.Ser133=
- Coding
- c.399T>G
- MANE Select
- NM_001330585
- dbSNP
- rs41311156
- Type
- single nucleotide variant
- Location
- chr1:52361052 (GRCh38)
- Gene constraint
- LOEUF 0.978 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
- Residue 133
- the 'disordered' region
Similar variants
- CC2D1B p.Gly790= Benign ★★ same type
- CC2D1B p.His674Tyr Likely benign ★★ same type
- CC2D1B p.Leu511= 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
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-ser133 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown