SAG p.Ser255=
c.765G>A · rs373623135 · VCV2192401
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00509%, nfe)
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 -6.6 | GERP -3.5 |
| Overall | ||
| CADD | 3.837 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00509%
European (non-Finnish) · 60/1,179,784 alleles
Filtering AF
0.00402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.00403%
65/1,613,676 alleles · very rare
exomes 61/1,461,546 · genomes 4/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00509% | 19,663 |
| South Asian | 0.00329% | 30,353 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| African / African-American | 0.00134% | 74,904 |
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.Ser255=
- Coding
- c.765G>A
- MANE Select
- NM_000541
- dbSNP
- rs373623135
- Type
- single nucleotide variant
- Location
- chr2:233331671 (GRCh38)
- Structure
- AlphaFold pLDDT 83.02 · 7 PDB
Similar variants
- SAG p.Ser255Leu Uncertain significance ★★ same residue
- SAG p.Ser255Trp 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
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-ser255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown