PIGN p.Tyr511Ter
c.1533T>A · rs2034805244 · VCV2831282
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
multiple congenital anomalies-hypotonia-seizures syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 17 of 31 |
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss · deltas |
| Pangolin | Δ0.31 | loss · gain 0.11 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.023 | GERP -3.2, phastCons 0.009 |
| Overall | ||
| CADD | 36.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- PIGN
- Protein
- p.Tyr511Ter
- Coding
- c.1533T>A
- MANE Select
- NM_176787
- dbSNP
- rs2034805244
- Type
- single nucleotide variant
- Location
- chr18:62109875 (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.Tyr511= Likely benign ★ same residue
- PIGN c.1251+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PIGN c.1252-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PIGN c.1434+5G>A Pathogenic/Likely pathogenic ★★ same condition
- PIGN c.1574+1G>A Likely pathogenic ★★ same condition
- PIGN c.1674+1G>A Likely pathogenic ★★ same condition
- PIGN c.1674+1G>C Pathogenic ★★ same condition
- PIGN c.1675-1G>T 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-tyr511ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown