CASQ1 p.Val348=
c.1044C>T · rs758981867 · VCV758748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 | GERP -2.2 |
| Overall | ||
| CADD | 10.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,870 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000831%
Overall
0.00144%
21/1,459,476 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,870 |
| European (non-Finnish) | 0.00161% | 61,994 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,418 |
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
- CASQ1
- Protein
- p.Val348=
- Coding
- c.1044C>T
- MANE Select
- NM_001231
- dbSNP
- rs758981867
- Type
- single nucleotide variant
- Location
- chr1:160199910 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.51 · 6 PDB
- Residue 348
- a β-strand
Similar variants
- CASQ1 p.Asp244Gly Pathogenic ★★ ⚠ same type
- CASQ1 c.279+1G>A Uncertain significance ★★ same type
- CASQ1 c.984+2T>G Uncertain significance ★★ same type
- CASQ1 c.985-1G>A Uncertain significance ★★ same type
- CASQ1 p.Ala115Val Uncertain significance ★★ ⚠ same type
- CASQ1 p.Ala172Pro Uncertain significance ★★ ⚠ same type
- CASQ1 p.Ala172Val Uncertain significance ★★ ⚠ same type
- CASQ1 p.Ala289Thr 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/casq1-p-val348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown