SAG p.Ser110=
c.330C>T · rs753704252 · VCV1926941
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00268%, afr)
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 1 | GERP -0.19, phastCons 1 |
| Overall | ||
| CADD | 9.231 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
African / African-American · 2/74,688 alleles
Filtering AF
0.000444%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000436%
7/1,605,754 alleles · very rare
exomes 6/1,453,604 · genomes 1/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00268% | 37,344 |
| European (non-Finnish) | 0.000425% | 235,264 |
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
- SAG
- Protein
- p.Ser110=
- Coding
- c.330C>T
- MANE Select
- NM_000541
- dbSNP
- rs753704252
- Type
- single nucleotide variant
- Location
- chr2:233320778 (GRCh38)
- Structure
- AlphaFold pLDDT 83.02 · 7 PDB
- Residue 110
- a β-strand
Similar variants
- SAG p.Ser110Asn Uncertain significance ★★ ⚠ same residue
- SAG c.1023-2A>G Likely pathogenic ★★ same type
- SAG c.1103-2A>C Pathogenic/Likely pathogenic ★★ same type
- SAG c.136+2T>C Likely pathogenic ★★ same type
- SAG c.136+2T>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.181+1G>A Likely pathogenic ★★ same type
- SAG c.182-2A>G Pathogenic/Likely pathogenic ★★ same type
- SAG c.376-2A>G Pathogenic/Likely 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/sag-p-ser110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown