CAVIN2 p.Lys173=
c.519A>G · rs61742216 · VCV782418
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.97%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.82 | GERP -3.3, phastCons 0.011 |
| Overall | ||
| CADD | 3.254 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.97%
African / African-American · 5,981/75,002 alleles
Filtering AF
7.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.74%
Overall
0.42%
6,770/1,613,768 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.97% | 13 |
| Remaining individualsnot grpmax-eligible | 0.546% | 183 |
| Admixed American | 0.452% | 221 |
| Middle Eastern | 0.248% | 404 |
| South Asian | 0.0165% | 6,071 |
| European (non-Finnish) | 0.0125% | 8,026 |
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
- CAVIN2
- Protein
- p.Lys173=
- Coding
- c.519A>G
- MANE Select
- NM_004657
- dbSNP
- rs61742216
- Type
- single nucleotide variant
- Location
- chr2:191836682 (GRCh38)
- Gene constraint
- LOEUF 1.593 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.48
Similar variants
- CAVIN2 p.Lys173Glu Uncertain significance ★ ⚠ same residue
- CAVIN2 p.Val66= Benign ★★ same type
- CAVIN2 p.Ala105Asp Uncertain significance ★ ⚠ same type
- CAVIN2 p.Ala137Val Uncertain significance ★ ⚠ same type
- CAVIN2 p.Ala309Thr Uncertain significance ★ ⚠ same type
- CAVIN2 p.Ala400Thr Uncertain significance ★ ⚠ same type
- CAVIN2 p.Arg131His Uncertain significance ★ ⚠ same type
- CAVIN2 p.Arg141Pro 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/cavin2-p-lys173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown