Is GOT2 p.Asn71= (c.213T>C) pathogenic?

GOT2 p.Asn71= (c.213T>C) is classified Benign in GOT2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-03). Common (popmax 80.7%, mid) — too common for a highly-penetrant pathogenic allele; Associated with developmental and epileptic encephalopathy, 82.

What condition is associated with GOT2 p.Asn71= (c.213T>C)?

GOT2 p.Asn71= (c.213T>C) is associated with developmental and epileptic encephalopathy, 82 (ClinVar).

GOT2 p.Asn71=

Q: How common is GOT2 p.Asn71= (c.213T>C) in the general population?

GOT2 p.Asn71= (c.213T>C) is common (popmax 80.7%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.213T>C · rs257636 · VCV1285302

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 80.7%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

developmental and epileptic encephalopathy, 82

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 -2.4	GERP -3.2
Overall
CADD	3.056	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 80.7% Middle Eastern · 4,883/6,054 alleles

Filtering AF 80.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 79.9%

Overall 64.5% 1,037,429/1,608,108 alleles · common exomes 932,073/1,456,140 · genomes 105,356/151,968 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	80.7%	1
African / African-American	80.6%	1
Ashkenazi Jewishnot grpmax-eligible	76.7%	1
Admixed American	74.3%	1
Remaining individualsnot grpmax-eligible	66.7%	1
European (non-Finnish)	63.2%	2
Amishnot grpmax-eligible	62.8%	2
South Asian	61.6%	2
Finnishnot grpmax-eligible	59.8%	2
East Asian	57.9%	2

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.Asn71=
Coding: c.213T>C
MANE Select: NM_002080
dbSNP: rs257636
Type: single nucleotide variant
Location: chr16:58723779 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI 0.49 (gnomAD)
Structure: AlphaFold pLDDT 94.77 · 3 PDB

Full GOT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 82 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GOT2 p.Arg262Gly Likely pathogenic ★★ same condition
GOT2 p.Gly366Val Likely pathogenic ★★ same condition
GOT2 p.Ala89Ser Uncertain significance ★★ ⚠ same condition
GOT2 p.Asp190Val Uncertain significance ★★ ⚠ same condition
GOT2 p.Asp197Asn Uncertain significance ★★ ⚠ same condition
GOT2 p.Leu362Phe Uncertain significance ★★ ⚠ same condition
GOT2 p.Pro78Leu Uncertain significance ★★ ⚠ same condition
GOT2 p.Val294Leu Uncertain significance ★★ same condition

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-asn71 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown