Is OGDHL p.Val488= (c.1464T>C) pathogenic?

OGDHL p.Val488= (c.1464T>C) is classified Pathogenic in OGDHL (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-01-14). Absent from gnomAD v4.1; Associated with Yoon-Bellen neurodevelopmental syndrome.

What condition is associated with OGDHL p.Val488= (c.1464T>C)?

OGDHL p.Val488= (c.1464T>C) is associated with Yoon-Bellen neurodevelopmental syndrome (ClinVar).

How common is OGDHL p.Val488= (c.1464T>C) in the general population?

OGDHL p.Val488= (c.1464T>C) is absent from gnomAD v4.1 (gnomAD).

OGDHL p.Val488=

c.1464T>C · rs2133028735 · VCV1334179

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Yoon-Bellen neurodevelopmental syndrome

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 -2.6	GERP -4
Overall
CADD	0.122	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: OGDHL
Protein: p.Val488=
Coding: c.1464T>C
MANE Select: NM_018245
dbSNP: rs2133028735
Type: single nucleotide variant
Location: chr10:49745810 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.44
Residue 488: a UniProt-annotated variant site (in yobeln; likely pathogenic; fails to rescue knockout-induced defects in a zebrafish disease model)

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

Disease context

Yoon-Bellen neurodevelopmental syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

OGDHL p.Arg351Trp Uncertain significance ★★ same condition
OGDHL p.Arg684Cys Uncertain significance ★★ ⚠ same condition
OGDHL p.Arg758Gln Uncertain significance ★★ ⚠ same condition
OGDHL p.Glu468Gln Uncertain significance ★★ ⚠ same condition
OGDHL p.Phe265Leu Uncertain significance ★★ ⚠ same condition
OGDHL c.1862-2A>G Likely pathogenic ★ same condition
OGDHL c.2140+1G>A Likely pathogenic ★ same condition
OGDHL p.Arg299Gly Likely pathogenic ★ 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/ogdhl-p-val488 (accessed [today's date]).

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