ATP6V0A2 p.Phe412fs
c.1236del · VCV3372310
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ATP6V0A2
- Protein
- p.Phe412fs
- Coding
- c.1236del
- MANE Select
- NM_012463
- Type
- Deletion
- Location
- chr12:123744245 (GRCh38)
- Gene constraint
- LOEUF 0.603 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 81.94
Similar variants
- ATP6V0A2 c.117+1del Likely pathogenic ★★ same type
- ATP6V0A2 p.Asn43_Val44insTer Pathogenic/Likely pathogenic ★★ same type
- ATP6V0A2 c.1724+20del Benign ★★ same type
- ATP6V0A2 c.2466-3del Benign/Likely benign ★★ same type
- ATP6V0A2 c.2466-4_2466-3del Benign/Likely benign ★★ same type
- ATP6V0A2 c.522-13del Benign/Likely benign ★★ same type
- ATP6V0A2 c.1501_1514+15del Likely pathogenic ★ same type
- ATP6V0A2 p.Ala798fs Likely pathogenic ★ 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/atp6v0a2-p-phe412fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown