CAPZA2 c.720+1G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,532,076)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ0.85 | donor loss · deltas |
| Pangolin | Δ0.85 | loss · gain 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,532,076). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CAPZA2
- Coding
- c.720+1G>A
- MANE Select
- NM_006136
- Type
- single nucleotide variant
- Location
- chr7:116916123 (GRCh38)
- Gene constraint
- LOEUF 0.444 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 93.11
Similar variants
- CAPZA2 p.Arg259Cys Likely pathogenic ★ same type
- CAPZA2 p.Lys256Glu Pathogenic ★ same type
- CAPZA2 c.103+1G>A Uncertain significance ★ same type
- CAPZA2 c.585+1G>T Uncertain significance ★ same type
- CAPZA2 c.585+2T>G Uncertain significance ★ same type
- CAPZA2 p.Ala116Thr Uncertain significance ★ ⚠ same type
- CAPZA2 p.Ala130Val Uncertain significance ★ ⚠ same type
- CAPZA2 p.Ala18Thr 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/capza2-c-720-plus-1g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown