CASQ2 p.Val80=
c.240G>A · rs2101101070 · VCV1329102
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0066%, sas)
Conditions
3
cardiomyopathy
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 2.8 | GERP 0.68, phastCons 1 |
| Overall | ||
| CADD | 11.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0066%
South Asian · 6/90,934 alleles
Filtering AF
0.00287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.000411%
6/1,459,912 alleles · very rare
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
- CASQ2
- Protein
- p.Val80=
- Coding
- c.240G>A
- MANE Select
- NM_001232
- dbSNP
- rs2101101070
- Type
- single nucleotide variant
- Location
- chr1:115744907 (GRCh38)
- Gene constraint
- LOEUF 1.322 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.63 · 4 PDB
- Residue 80
- an α-helix
Similar variants
- CASQ2 c.235-2A>G Likely pathogenic ★★ same condition
- CASQ2 c.319+2T>G Likely pathogenic ★★ same condition
- CASQ2 c.320-2A>G Pathogenic ★★ same condition
- CASQ2 c.420+1G>A Likely pathogenic ★★ same condition
- CASQ2 c.532+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CASQ2 c.533-2A>G Likely pathogenic ★★ same condition
- CASQ2 c.606+1G>C Pathogenic/Likely pathogenic ★★ same condition
- CASQ2 c.606+2T>A Likely pathogenic ★★ same condition
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/casq2-p-val80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown