CASQ2 p.Asp381=
c.1143T>C · rs2464831115 · VCV1731950
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -4.7 | GERP -5.6 |
| Overall | ||
| CADD | 0.148 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/90,692 alleles
Filtering AF
0.000434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000316%
Overall
0.000689%
11/1,597,616 alleles · very rare
exomes 11/1,445,398 · genomes 0/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 90,692 |
| European (non-Finnish) | 0.000858% | 116,512 |
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.Asp381=
- Coding
- c.1143T>C
- MANE Select
- NM_001232
- dbSNP
- rs2464831115
- Type
- single nucleotide variant
- Location
- chr1:115701298 (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 381
- the 'disordered' region
Similar variants
- 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
- CASQ2 p.Tyr55Cys Pathogenic/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-asp381 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown