PGAP1 c.860+99del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 16%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| Splice region | donor +99 | deep intronic (+99 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Non-coding constraint | Z 1.39 | 1 kb window · o/e 0.90 · regional · uncalibrated |
| Overall | ||
| CADD | 0.602 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16%
South Asian · 7,245/45,370 alleles
Filtering AF
15.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.5%
Overall
12.2%
75,020/616,486 alleles · common
exomes 74,791/497,640 · genomes 229/118,846 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 16% | 6 |
| Remaining individualsnot grpmax-eligible | 14.4% | 7 |
| East Asian | 13.3% | 8 |
| Middle Eastern | 13.1% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 13% | 8 |
| European (non-Finnish) | 12.8% | 8 |
| Finnishnot grpmax-eligible | 10.6% | 9 |
| Admixed American | 9.82% | 10 |
| African / African-American | 3.86% | 26 |
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
- PGAP1
- Coding
- c.860+99del
- MANE Select
- NM_024989
- dbSNP
- rs369035974
- Type
- Deletion
- Location
- chr2:196898218 (GRCh38)
- Gene constraint
- LOEUF 0.691 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 89.15
Similar variants
- PGAP1 p.Leu681fs Pathogenic/Likely pathogenic ★★ same type
- PGAP1 c.1089+5del Likely pathogenic ★ same type
- PGAP1 c.1426+1del Likely pathogenic ★ same type
- PGAP1 p.Asn223fs Pathogenic ★ same type
- PGAP1 p.Asn7fs Pathogenic ★ same type
- PGAP1 p.Asp192fs Likely pathogenic ★ same type
- PGAP1 p.Cys623fs Pathogenic ★ same type
- PGAP1 p.Lys308fs 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/pgap1-c-860-plus-99del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown