CAST p.Asp652=
c.1956T>C · rs866299479 · VCV3024666
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.15%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.256 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.7 | GERP -2.8, phastCons 0.027 |
| Overall | ||
| CADD | 4.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.15%
Middle Eastern · 9/6,020 alleles
Filtering AF
0.078%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0582%
Overall
0.000811%
13/1,603,782 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.15% | 669 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,102 |
| European (non-Finnish) | 0.00017% | 586,875 |
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
- CAST
- Protein
- p.Asp652=
- Coding
- c.1956T>C
- dbSNP
- rs866299479
- Type
- single nucleotide variant
- Location
- chr5:96765244 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.67
- Residue 652
- the 'disordered' region
Similar variants
- PCSK1 p.Gly652Arg Uncertain significance ★ ⚠ same residue
- PCSK1 p.Gly652= Likely benign ★ same residue
- PCSK1 p.Lys286Ter Pathogenic/Likely pathogenic ★★ same type
- CAST p.Ala329Gly Uncertain significance ★★ ⚠ same type
- CAST p.Asp160Val Uncertain significance ★★ ⚠ same type
- CAST p.Gln731His Uncertain significance ★★ ⚠ same type
- CAST p.Glu296Gly Uncertain significance ★★ ⚠ same type
- CAST p.Ile274Val 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/cast-p-asp652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown