CACNG2 p.Val193=
c.579C>T · rs149442040 · VCV739995
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0286%, nfe)
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 4.1 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 12.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0286%
European (non-Finnish) · 338/1,180,008 alleles
Filtering AF
0.0261%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0251%
Overall
0.0222%
359/1,614,024 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0286% | 3,491 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,905 |
| African / African-American | 0.00534% | 18,734 |
| Admixed American | 0.00167% | 60,004 |
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
- CACNG2
- Protein
- p.Val193=
- Coding
- c.579C>T
- MANE Select
- NM_006078
- dbSNP
- rs149442040
- Type
- single nucleotide variant
- Location
- chr22:36564744 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.26 · 5 PDB
Similar variants
- CACNG2 p.Ala100Ser Uncertain significance ★★ ⚠ same type
- CACNG2 p.Ala214Thr Uncertain significance ★★ ⚠ same type
- CACNG2 p.Arg319Pro Uncertain significance ★★ ⚠ same type
- CACNG2 p.Gln298Arg Uncertain significance ★★ ⚠ same type
- CACNG2 p.Glu126Lys Uncertain significance ★★ ⚠ same type
- CACNG2 c.212-12C>A Likely benign ★★ same type
- CACNG2 c.436+1G>A Uncertain significance ★ same type
- CACNG2 p.Ala103Thr 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/cacng2-p-val193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown