OGDHL p.Phe889=
c.2667C>T · rs151304962 · VCV710350
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.187%, nfe)
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 2.1 | GERP 0.95, phastCons 1 |
| Overall | ||
| CADD | 8.951 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.187%
European (non-Finnish) · 2,211/1,180,036 alleles
Filtering AF
0.181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.178%
Overall
0.142%
2,291/1,613,940 alleles · rare
exomes 2,151/1,461,756 · genomes 140/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.187% | 534 |
| Remaining individualsnot grpmax-eligible | 0.0864% | 1,157 |
| African / African-American | 0.0227% | 4,407 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
| Finnishnot grpmax-eligible | 0.00626% | 15,985 |
| Admixed American | 0.00333% | 30,004 |
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
- OGDHL
- Protein
- p.Phe889=
- Coding
- c.2667C>T
- MANE Select
- NM_018245
- dbSNP
- rs151304962
- Type
- single nucleotide variant
- Location
- chr10:49736444 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.44
- Residue 889
- a UniProt-annotated variant site (in yobeln; likely pathogenic; fails to rescue knockout-induced defects in a zebrafish disease model)
Similar variants
- OGDHL p.Arg351Trp Uncertain significance ★★ same type
- OGDHL p.Arg636Trp Uncertain significance ★★ ⚠ same type
- OGDHL p.Arg684Cys Uncertain significance ★★ ⚠ same type
- OGDHL p.Arg758Gln Uncertain significance ★★ ⚠ same type
- OGDHL p.Glu468Gln Uncertain significance ★★ ⚠ same type
- OGDHL p.Gly774Asp Uncertain significance ★★ ⚠ same type
- OGDHL p.Phe265Leu Uncertain significance ★★ ⚠ same type
- OGDHL p.Ser31Asn 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/ogdhl-p-phe889 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown