VAC14 p.Ser252=
c.756C>T · rs185169828 · VCV1905089
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 0.28 | GERP -0.55, phastCons 0.95 |
| Overall | ||
| CADD | 9.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,024 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00578%
Overall
0.00062%
10/1,614,134 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,669 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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
- VAC14
- Protein
- p.Ser252=
- Coding
- c.756C>T
- MANE Select
- NM_018052
- dbSNP
- rs185169828
- Type
- single nucleotide variant
- Location
- chr16:70783088 (GRCh38)
- Gene constraint
- LOEUF 0.681 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.63 · 1 PDB
Similar variants
- VAC14 p.Ser252Tyr Benign ★ same residue
- VAC14 p.Leu308Ter Pathogenic/Likely pathogenic ★★ same type
- VAC14 p.Ala474Thr Uncertain significance ★★ ⚠ same type
- VAC14 p.Arg110His Uncertain significance ★★ ⚠ same type
- VAC14 p.Arg434Trp Uncertain significance ★★ same type
- VAC14 p.Arg438Gln Uncertain significance ★★ ⚠ same type
- VAC14 p.Arg438Trp Uncertain significance ★★ ⚠ same type
- VAC14 p.Arg623Cys 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/vac14-p-ser252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown