GOT2 p.Ser416=
c.1248C>T · rs115220077 · VCV733891
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.73%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.5 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 9.916 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.73%
African / African-American · 2,049/75,020 alleles
Filtering AF
2.63%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.59%
Overall
0.143%
2,305/1,614,046 alleles · low-frequency
exomes 1,081/1,461,760 · genomes 1,224/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.73% | 37 |
| Middle Eastern | 0.247% | 404 |
| Remaining individualsnot grpmax-eligible | 0.168% | 595 |
| Admixed American | 0.128% | 779 |
| European (non-Finnish) | 0.00466% | 21,454 |
| South Asian | 0.00439% | 22,770 |
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
- GOT2
- Protein
- p.Ser416=
- Coding
- c.1248C>T
- MANE Select
- NM_002080
- dbSNP
- rs115220077
- Type
- single nucleotide variant
- Location
- chr16:58708216 (GRCh38)
- Gene constraint
- LOEUF 0.591 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 94.77 · 3 PDB
- Residue 416
- an α-helix
Similar variants
- GOT2 p.Arg262Gly Likely pathogenic ★★ same type
- GOT2 p.Gly366Val Likely pathogenic ★★ same type
- GOT2 p.Ala89Ser Uncertain significance ★★ ⚠ same type
- GOT2 p.Arg325Gln Uncertain significance ★★ ⚠ same type
- GOT2 p.Asp190Val Uncertain significance ★★ ⚠ same type
- GOT2 p.Asp197Asn Uncertain significance ★★ ⚠ same type
- GOT2 p.Gln357Glu Uncertain significance ★★ ⚠ same type
- GOT2 p.Gln372Arg 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/got2-p-ser416 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown