Is OGDH p.Pro480= (c.1440C>T) pathogenic?

OGDH p.Pro480= (c.1440C>T) is classified Likely benign in OGDH (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-04). Ultra-rare (popmax 0.0178%, eas); Associated with oxoglutaricaciduria.

What condition is associated with OGDH p.Pro480= (c.1440C>T)?

OGDH p.Pro480= (c.1440C>T) is associated with oxoglutaricaciduria (ClinVar).

How common is OGDH p.Pro480= (c.1440C>T) in the general population?

OGDH p.Pro480= (c.1440C>T) is ultra-rare (popmax 0.0178%, eas) (gnomAD).

How is Oxoglutaric aciduria inherited?

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

OGDH p.Pro480=

c.1440C>T · rs769704074 · VCV1597659

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, eas)

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 -9.7	GERP -4
Overall
CADD	1.221	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0178% East Asian · 8/44,902 alleles

Filtering AF 0.00883% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00641%

Overall 0.000991% 16/1,613,988 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0178%	5,613
Remaining individualsnot grpmax-eligible	0.0032%	31,241
African / African-American	0.00133%	74,924
European (non-Finnish)	0.000424%	235,999

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.Pro480=
Coding: c.1440C>T
MANE Select: NM_002541
dbSNP: rs769704074
Type: single nucleotide variant
Location: chr7:44693929 (GRCh38)
Gene constraint: LOEUF 0.415 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.73 · 3 PDB
Residue 480: an α-helix

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-pro480 (accessed [today's date]).

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