PIGN p.Ser535=
c.1605A>C · rs755115652 · VCV1675709
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00347%, sas)
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 -3.8 | GERP -3.7 |
| Overall | ||
| CADD | 3.395 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00347%
South Asian · 3/86,432 alleles
Filtering AF
0.000922%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000456%
Overall
0.000315%
5/1,587,818 alleles · very rare
exomes 5/1,435,526 · genomes 0/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00347% | 28,811 |
| European (non-Finnish) | 0.000171% | 583,189 |
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.Ser535=
- Coding
- c.1605A>C
- MANE Select
- NM_176787
- dbSNP
- rs755115652
- Type
- single nucleotide variant
- Location
- chr18:62107055 (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.Ser535Ter Pathogenic ★ same residue
- PIGN p.Ser535Pro Uncertain significance ★ ⚠ same residue
- PIGN c.1251+1G>A Pathogenic/Likely pathogenic ★★ same type
- PIGN c.1252-2A>G Pathogenic/Likely pathogenic ★★ same type
- PIGN c.1434+5G>A Pathogenic/Likely pathogenic ★★ same type
- PIGN c.1574+1G>A Likely pathogenic ★★ same type
- PIGN c.1674+1G>A Likely pathogenic ★★ same type
- PIGN c.1674+1G>C 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/pign-p-ser535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown