VPS16 p.Ser72=
c.216C>T · rs3818605 · VCV1242073
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 26.5%, sas) — too common for a highly-penetrant pathogenic allele
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 -8.5 | GERP -5.4 |
| Overall | ||
| CADD | 3.925 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
26.5%
South Asian · 24,125/91,066 alleles
Filtering AF
26.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 26.1%
Overall
15.4%
248,388/1,613,888 alleles · common
exomes 228,823/1,461,774 · genomes 19,565/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 26.5% | 4 |
| East Asian | 20.1% | 5 |
| Finnishnot grpmax-eligible | 17.2% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 17% | 6 |
| Amishnot grpmax-eligible | 16.3% | 6 |
| Remaining individualsnot grpmax-eligible | 15.7% | 6 |
| Middle Eastern | 15.6% | 6 |
| European (non-Finnish) | 15.1% | 7 |
| Admixed American | 12% | 8 |
| African / African-American | 4.27% | 23 |
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
- VPS16
- Protein
- p.Ser72=
- Coding
- c.216C>T
- MANE Select
- NM_022575
- dbSNP
- rs3818605
- Type
- single nucleotide variant
- Location
- chr20:2860127 (GRCh38)
- Gene constraint
- LOEUF 0.813 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.35 · 1 PDB
Similar variants
- VPS16 c.1331+2T>C Likely pathogenic ★★ same type
- VPS16 p.Arg635Ter Pathogenic ★★ same type
- VPS16 p.Tyr445Ter Pathogenic ★★ same type
- VPS16 p.Tyr463Ter Pathogenic/Likely pathogenic ★★ same type
- VPS16 c.1332-1G>T Uncertain significance ★★ same type
- VPS16 p.Arg129Gln Uncertain significance ★★ ⚠ same type
- VPS16 p.Arg262Trp Uncertain significance ★★ ⚠ same type
- VPS16 p.Arg273Cys Uncertain significance ★★ ⚠ 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/vps16-p-ser72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown