GOT2 p.Asn417=
c.1251C>T · rs765079791 · VCV2176327
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -7.6 | GERP -3.7 |
| Overall | ||
| CADD | 1.203 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,878 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00062%
10/1,613,968 alleles · very rare
exomes 9/1,461,784 · genomes 1/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,959 |
| African / African-American | 0.00267% | 37,458 |
| European (non-Finnish) | 0.000424% | 235,998 |
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.Asn417=
- Coding
- c.1251C>T
- MANE Select
- NM_002080
- dbSNP
- rs765079791
- Type
- single nucleotide variant
- Location
- chr16:58708213 (GRCh38)
- Gene constraint
- LOEUF 0.591 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 94.77 · 3 PDB
- Residue 417
- 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-asn417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown