CAV2 p.Thr146=
c.438G>A · VCV3995905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -0.91 | GERP -4 |
| Overall | ||
| CADD | 1.562 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00318%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00286%
Overall
0.00366%
59/1,613,952 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| European (non-Finnish) | 0.00415% | 24,079 |
| Admixed American | 0.00333% | 30,005 |
| East Asian | 0.00223% | 44,878 |
| African / African-American | 0.00133% | 75,018 |
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
- CAV2
- Protein
- p.Thr146=
- Coding
- c.438G>A
- MANE Select
- NM_001233
- Type
- single nucleotide variant
- Location
- chr7:116506070 (GRCh38)
- Gene constraint
- LOEUF 0.938 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 78.26
Similar variants
- CAV2 p.Thr146Met Uncertain significance ★ ⚠ same residue
- CAV2 p.Ser147= Benign ★★ same type
- CAV2 p.Ala8Val Uncertain significance ★ ⚠ same type
- CAV2 p.Arg40Gln Uncertain significance ★ ⚠ same type
- CAV2 p.Asp17Ala Uncertain significance ★ ⚠ same type
- CAV2 p.Asp17Tyr Uncertain significance ★ ⚠ same type
- CAV2 p.Asp55Asn Uncertain significance ★ ⚠ same type
- CAV2 p.Cys151Tyr 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/cav2-p-thr146 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown