PIGA p.Ser244=
c.732T>C · rs1433819812 · VCV2022199
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000472%, nfe)
Conditions
1
multiple congenital anomalies-hypotonia-seizures syndrome 2
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 8.1 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 9.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000472%
European (non-Finnish) · 4/847,506 alleles
Filtering AF
0.00011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.5e-05%
Overall
0.000349%
4/1,147,195 alleles · very rare
exomes 3/1,034,837 · genomes 1/112,358 · joint denominator
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
- PIGA
- Protein
- p.Ser244=
- Coding
- c.732T>C
- MANE Select
- NM_002641
- dbSNP
- rs1433819812
- Type
- single nucleotide variant
- Location
- chrX:15326030 (GRCh38)
- Structure
- AlphaFold pLDDT 86.22
Similar variants
- PIGA p.Arg119Gln Pathogenic/Likely pathogenic ★★ same condition
- PIGA p.Arg119Trp Pathogenic/Likely pathogenic ★★ same condition
- PIGA p.Arg412Ter Pathogenic ★★ same condition
- PIGA p.Arg81His Likely pathogenic ★★ same condition
- PIGA p.Val329Ala Likely pathogenic ★★ same condition
- PIGA p.Val49Met Pathogenic/Likely pathogenic ★★ same condition
- PIGA c.982-3A>C Uncertain significance ★★ same condition
- PIGA p.Ala2Thr Uncertain significance ★★ ⚠ same condition
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-ser244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown