CASQ2 p.Asp349=
c.1047T>C · rs369982880 · VCV2565184
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
1
Cardiovascular phenotype
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 -3.5 | GERP -5.6 |
| Overall | ||
| CADD | 0.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,890 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.00031%
5/1,613,774 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,445 |
| South Asian | 0.0022% | 45,536 |
| Finnishnot grpmax-eligible | 0.00156% | 64,036 |
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.Asp349=
- Coding
- c.1047T>C
- MANE Select
- NM_001232
- dbSNP
- rs369982880
- Type
- single nucleotide variant
- Location
- chr1:115701394 (GRCh38)
- Gene constraint
- LOEUF 1.322 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.63 · 4 PDB
Similar variants
- CASQ2 p.Asp349Val Uncertain significance ★★ ⚠ same residue
- CASQ2 c.319+2T>G Likely pathogenic ★★ same condition
- CASQ2 c.420+1G>A Likely pathogenic ★★ same condition
- CASQ2 c.533-2A>G Likely pathogenic ★★ same condition
- CASQ2 c.939+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CASQ2 p.Arg33Ter Pathogenic/Likely pathogenic ★★ same condition
- CASQ2 p.Gln67Ter Pathogenic ★★ same condition
- CASQ2 p.Trp343Ter 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-asp349 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown