Is OGDH p.Asp596= (c.1788C>T) pathogenic?

OGDH p.Asp596= (c.1788C>T) is classified Likely benign in OGDH (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-26). Very rare (popmax 0.00668%, amr); Associated with oxoglutaricaciduria.

What condition is associated with OGDH p.Asp596= (c.1788C>T)?

OGDH p.Asp596= (c.1788C>T) is associated with oxoglutaricaciduria (ClinVar).

How common is OGDH p.Asp596= (c.1788C>T) in the general population?

OGDH p.Asp596= (c.1788C>T) is very rare (popmax 0.00668%, amr) (gnomAD).

How is Oxoglutaric aciduria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

OGDH p.Asp596=

c.1788C>T · rs756317172 · VCV2745793

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, amr)

Conditions

oxoglutaricaciduria

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 -8.7	GERP -4
Overall
CADD	1.65	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% Admixed American · 4/59,884 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000868% 14/1,613,646 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00668%	14,971
African / African-American	0.00534%	18,727
South Asian	0.0022%	45,518
Remaining individualsnot grpmax-eligible	0.0016%	62,462
Finnishnot grpmax-eligible	0.00156%	64,036
European (non-Finnish)	0.00017%	589,922

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: OGDH
Protein: p.Asp596=
Coding: c.1788C>T
MANE Select: NM_002541
dbSNP: rs756317172
Type: single nucleotide variant
Location: chr7:44696445 (GRCh38)
Gene constraint: LOEUF 0.415 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.73 · 3 PDB

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

Disease context

oxoglutaricaciduria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Oxoglutaric aciduria (Orphanet):

Inheritance: Autosomal recessive
Onset: Neonatal

Similar variants

OGDH p.Arg204Trp Uncertain significance ★★ ⚠ same condition
OGDH p.Asn709Ser Uncertain significance ★★ ⚠ same condition
OGDH p.Asp811Glu Uncertain significance ★★ ⚠ same condition
OGDH p.Lys532Arg Uncertain significance ★★ ⚠ same condition
OGDH p.Ser1023Leu Uncertain significance ★★ ⚠ same condition
OGDH p.Thr15Met Uncertain significance ★★ ⚠ same condition
OGDH p.Thr610Met Uncertain significance ★★ ⚠ same condition
OGDH p.Thr615Ile 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/ogdh-p-asp596 (accessed [today's date]).

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