PIGA p.Arg412=
c.1234C>A · rs387906726 · VCV681438
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 3.9 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 7.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PIGA
- Protein
- p.Arg412=
- Coding
- c.1234C>A
- MANE Select
- NM_002641
- dbSNP
- rs387906726
- Type
- single nucleotide variant
- Location
- chrX:15321727 (GRCh38)
- Structure
- AlphaFold pLDDT 86.22
- Residue 412
- a UniProt-annotated variant site (in mcahs2; decreased function in gpi anchor biosynthesis; does not fully restore gpi-anchored cd59 surface expression when transfected in piga-null cells; does not rescue defective hamp expression in piga-deficient cells overexpressing hjv, suggesting absent or reduced hjv anchorage at the cell membrane)
Similar variants
- PIGA p.Arg412Ter Pathogenic ★★ same residue
- PIGA p.Arg412Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- PIGA p.Arg119Gln Pathogenic/Likely pathogenic ★★ same type
- PIGA p.Arg119Trp Pathogenic/Likely pathogenic ★★ same type
- PIGA p.Arg81His Likely pathogenic ★★ same type
- PIGA p.Met37Val Likely pathogenic ★★ same type
- PIGA p.Val329Ala Likely pathogenic ★★ same type
- PIGA p.Val49Met Pathogenic/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/piga-p-arg412 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown