PIGN p.Val698del
c.2091_2093del · rs1167158496 · VCV520603
Likely pathogenic
Multiple submitters
Classification
Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00034%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.087 | GERP -0.8, phastCons 0.19 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00034%
European (non-Finnish) · 4/1,176,810 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,610,176 alleles · very rare
exomes 4/1,458,078 · genomes 0/152,098 · 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
- PIGN
- Protein
- p.Val698del
- Coding
- c.2091_2093del
- MANE Select
- NM_176787
- dbSNP
- rs1167158496
- Type
- Deletion
- Location
- chr18:62095935 (GRCh38)
- Gene constraint
- LOEUF 1.46 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.33
Similar variants
- PIGN p.Val698Met Uncertain significance ★★ ⚠ same residue
- PIGN c.2620-5del Benign/Likely benign ★★ same condition
- PIGN p.Val698Gly Uncertain significance ★ ⚠ same residue
- PIGN c.1675-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PIGN p.Arg613Ter Pathogenic/Likely pathogenic ★★ same condition
- PIGN p.Arg785His Likely pathogenic ★★ same condition
- PIGN p.Arg95Trp Pathogenic/Likely pathogenic ★★ same condition
- PIGN p.Leu311Trp Pathogenic/Likely pathogenic ★★ 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/pign-p-val698del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown